Axiope Catalyzer is a combined data management, data sharing and data publication tool. Catalyzer lets you enter, edit, browse, search and export your own structured information - it's more powerful than spreadsheets, more structured than documents and way simpler than databases.

If you'd like to get up and running quickly with the software, this chapter shows you how to:

• View the example catalogs
• Make a catalog of data files
• Create a new catalog from scratch

The rest of the guide...

The next chapter, Introducing Catalyzer includes a more extensive introduction to what you can use Catalyzer for, and describes what "catalogs", "records" and "classes" are exactly.

Chapter 3, Making Catalogs shows in detail how to create and edit catalogs of your own information. Chapter 4, Spreadsheet / table mode shows how you can use Catalyzer as a more powerful alternative to spreadsheets, with a similar user interface. Chapter 5, Searching, filtering and browsing shows how to use the Catalyzer features for simple and sophisticated searching and sorting of your data.

Chapter 6, Importing and exporting details how to build catalogs from data you already have on hard disk or CD. Chapter 7, Creating web pages shows how any catalog can be turned into a set of structured web pages just by pressing the "Publish" button.

Chapter 8, Advanced Features describes the more advanced features built into catalyzer including template catalogs, required fields and user defined types. Chapter 9, Reference includes details of all the different field types and options, for reference purposes.

Chapter 10 gives some all-important ideas on How Catalyzer can fit in with existing workflows by providing some common example uses.

The final chapters cover Licenses, Hints, Tips and Troubleshooting and a Technical appendix.

When you first start Catalyzer, you'll see the welcome screen below:

The quickstart screen

The options let you create a new empty catalog, create a catalog by importing data from a directory, or open a built in example catalog. There are also two links to more help: view quickstart help (shows this document), or view online tutorials.

The online tutorials (at www.axiope.com/tutorials) include animated demonstrations walking you through how to use Catalyzer, and may be helpful to check alongside this user guide.

You can show the quickstart screen at any time from the File menu:

The quickstart screen is also available from the File menu

Catalyzer comes with a number of built-in example catalogs. The following steps show how to view them and find your way around the software.

A number of example catalogs are available from the Help menu

Start by loading an example catalog. For example, select Help>Example Catalogs... and then select the general folder and mountains.axz. You can explore the catalog using the tree on the left. More information about records and editing options are available from the context-sensitive menu. The menu can be raised by right-clicking on a folder (Window/Linux) or CTRL-clicking (Mac OS). A catalog can be thought of as a collection of tables of different sorts. Here, the rows in a table are termed "records", and the column headings that specify what each value in a row is are termed "classes". There are two main ways to view and edit records: as a table with many records on one page, one record per row; or as a a form with labels on the left and values on the right. If you select the "Photos" folder from the mountains catalog, you can use the little box icons at the bottom right to change the view. Double-click on a single photo record to see it in the form view. A single element of a class is termed a "field". It has a name (the label at the top of a column in a table view) and it specifies what type of data the record should contain for that item. In the form view there is one field per row. The name is on the left and the values for the active record are on the right. These can be edited in different ways according to the type of field. New records can be added to the catalog with the Add Using Class menu option or the Add, , toolbar button. The Delete option and button, , removes the selected record. You can also edit the classes in the catalog. Any changes you make apply to all records of that class. First press the Class Window, , button (or select View > Class from the main menu) to switch Catalyzer into class editing mode. You get a new panel on the right showing the properties of the selected field. You can add new fields with the Add Field icon. After adding a field, you can change its type with the controls on the right. To return to data entry mode use the Catalog, , toolbar button (or View>Catalog from the main menu). You can search and browse with the Edit>Search and Edit>Browse menu options.

Many features in Catalyzer use a context sensitive menu which is raised by right-clicking (ctrl-click on Mac). For example, to import data from the file system, right-click on a folder in the catalog tree and select: Import>Folder.... When you first start using Catalyzer, there will be a root folder called untitled with a folder icon, , beside it in the Catalog panel on the left of the main window.

Mac OS X users : to raise the context sensitive menu use CTRL-click.

Catalyzer can create a catalog of the files you have on your hard disk or CD. The catalog structure will match the structures of folders and subfolders you already have. For images, Catalyzer will create thumbnails in the catalog. You can add extra information to that automatically extracted from the files - e.g. notes and other annotation.

Import data from a folder using the File : Import menu

The import dialog lets you select the folder to import (click the Browse button)

Select File>New from the main menu. Select File>Import>Folder... Press the Browse button to pick a folder on your computer that contains images or data that you would like to catalog. Catalyzer goes into the subfolders, so if you pick a CD drive, for example, then the catalog that is created will hold records for everything on the CD. Close the progress dialog when it finishes importing. Catalyzer should create a record for each data file, and folders to match your directory structure. The names for records and folders in the catalog will be the same as the corresponding files on the file system. Switch to class editing mode ( Class Window button on the toolbar). Select a record to be extended. Press the Add button on the middle panel toolbar to add an extra field. Change the Field Name on the right hand panel from "Field" to "Quality". Add another field with the Add, , button. Then change its name to "notes" and this time also set the Field Type to Text Box. Switch back to record editing mode ( Catalog Window button on the toolbar). Enter some values for the Quality field you've just created for different records. Publish to website with Publish>Publish Catalog... from the main menu. Press the Publish button. Close the progress dialog when it finishes. Press the View... button in the publish catalog dialog to see the generated website in your browser.

This example shows how to create a new catalog, step by step. The catalog will contain records of three different types for holding data about experiments, protocols, and samples. There will be three distinct classes called "Experiments", "Protocols" and "Samples", and can be any number of records of each class.

This example is relevant if you'd like to use Catalyzer as an electronic notebook for gathering structured information - it also introduces the underlying concepts of Catalyzer.

Catalyzer operates in two modes - Catalog editing mode and Class editing mode. Catalog editing mode is for changing the content of the catalog; class editing mode is for changing the structure. You can switch between modes using the View>Catalog and View>Class main menu options, or the buttons on the toolbar. The section on switching Catalog modes has more details.

Start by creating an empty catalog File>New Start with an empty catalog This catalog is going to contain details of Experiments, Protocols and Samples, so start by creating separate folders for these. right-click (CTRL-click on Mac) on the root folder, and Add Using Class>Folder:- Add a folder Rename the folder as Experiments (double-click on name) Add extra folders for Samples and Protocols. You can either do this as before (right-click : Add), or you can just press Enter again after typing in the Experiments name to add an extra folder. Three folders The next step is to tell Catalyzer what information is relevant to include about Experiments, Samples and Protocols. The specification of what is needed for each type of record is called a Class in Catalyzer. Switch to the Class Window to add/edit classes. Switching to the Class Window Switching to the Class Window using the toolbar Compared with the Catalog Window, the Class Window has two additional panes; at the bottom left is a list of Classes (initially just Folder and Record), and on the right hand side is the Field Details Panel, containing details of an individual field of a class. The Class window To add the Classes for Experiment, Sample and Protocol, click the Add button in the Classes list (or select Add from the right-click menu). Adding a new class Renaming the new class You can add the other classes (Protocol and Sample) by pressing Enter after you've renamed the first. Added all three classes The next step is to add the Fields for the classes. Select the Experiment class in the list, and then add a field using the middle panel Add button. Adding a field to the Experiment class Adding and renaming fields in the Experiment class Add as many fields as you need to record the relevant information for a single experiment. Repeat the process to add fields to Protocol and Sample classes (Select the class in the Classes list at the bottom left, add fields using the button on the middle panel, and set the field name on the right hand panel). If you want to have multi-line entry for a field, change the field type to "Text Box":- Set the Field Type to 'Text Box' to add a multi-line description field For Samples, you might want to keep track of their location (perhaps room, freezer, shelf). There could be a restricted choice of different rooms. In this case you can simplify the data entry process by converting the room field to a Radio Buttons push button: Setting up the Sample class. Initially the Field Type is 'Text' Switching the Field Type to 'Radio Buttons' lets you create a menu of buttons Having created the necessary classes, you can now start adding some different Experiment, Protocol and Sample records to the catalog. First, switch back to Catalog mode. Switching back to Catalog Editing Mode To add an Experiment to the Experiments folder, use right-click Add Using Class>Experiment Add an Experiment to the Experiments folder Once you have added a record, you can enter data for the fields you created:- Adding details for an Experiment If you need to change fields, return to the Class Window and add/remove them. You can add entries for the different Samples and Protocols in the same way. This Sample record specifies the room and supplier It is often useful to make links between records. For example, there could be a link to a Protocol from each Experiment record. To do this, switch back to the Class window and add a field of type Reference to class Protocol. Adding a Protocol reference from the Experiment Clicking on the browse button (highlighted below) shows a reference chooser which lets you select the target protocol: Selecting the protocol for an experiment Clicking the "+" button next to the reference expands it inline, so you can see the details for the protocol next to the experiment: The experiment record linked to its protocol It is also useful to link to data files and documents. This can be done with the Resource field type. For example, to add a link to a Word document describing a protocol: The protocol record linked to a document

Once you have created a number of useful classes (such as the Experiment, Sample and Protocol classes described above), you can reuse them in multiple catalogs. Existing classes can be imported into a new catalog by selecting File>Import>Classes and types from the main File menu.

Catalyzer has a built in web server which lets you browse and search your catalogs using a web browser.

Load a catalog (Help > Example Catalogs > General > Mountains). Save a local copy of the catalog. (File > Save As...). Type "mountains" as the filename. You can view the catalog in the web server using (Web Server>View In Server). A dialog with a progress bar will appear the first time, as the web server starts up. Close this window once the web server has started. You can explore the catalog via a web browser using the tree on the left and you can search and browse catalogs just as you can in Catalyzer. Your colleagues will also be able to view your catalogs by entering the URL shown at the top (http://...:5151/) in their own browser.

By default, when you start up the Web Server, catalogs are accessible to any computer on the network. You can use passwords or address ranges to restrict access to catalogs. The configuration controls are accessible from the Home and Admin links on the Catalyzer Web webpage.

Viewing a catalog using Catalyzer Web Server

Catalyzer is a cataloging system that combines selected features from spreadsheets, documents and databases. Perhaps the closest analogy is with a library catalog that holds information about different types of item (books, journals, electronic resources et al). For each type, a particular set of information is needed - e.g. for a book, the authors, title, ISBN. For a journal, the title, volume, issue, ISSN. Then for each item (be it a journal or a book), there is a catalog entry (what used to be a record card) with the required values on it.

With Catalyzer, you can set up the different types and specify what pieces of information belong with each one. Or you can let Catalyzer create some basic types for you and then just extend these as and when you need to. The second approach is ideal if you want to archive the contents of folders on your hard disk or on CDs. The first approach applies if you want to enter new data from scratch in a structured fashion.

This section outlines some common approaches to data management which most people currently use, and shows how with Catalyzer things can be better.

Filenames / folders

Most people store information about files by giving them coded names, like: SCP_076_GX_rat_tty.dat and putting them into directories like: data/jan04/expts/run2/

Catalyzer will import all this information into a catalog, so you can search across all your data. The Catalyzer catalogs will also preserve the structure of folders and subfolders you have. With Catalyzer you can then add as much human readable annotation to the data files (e.g. paragraphs of notes, specifics of the experiments. You can also add in the links between files (e.g. explicitly link the raw data files to the analysis files). If you need to share your data with other people, a Catalyzer catalog will be a lot easier for them to understand than a filename like SCP_076_GX_rat_tty.dat, especially as you can publish a catalog as a website. Catalyzer will also dive into your data files and extract extra information and thumbnails embedded within, giving you a richer catalog of your data.

Spreadsheets

Many people store tabular data in spreadsheets. This is convenient to create and enter data - but it can be hard to search and sort across multiple spreadsheets. Spreadsheets also don't deal well with links and cross references between different worksheets, or with links to external files and images.

Catalyzer interacts very smoothly with spreadsheets - you can copy and paste tables between a spreadsheet and Catalyzer. As Catalyzer has a familiar hierarchical structure, you can store multiple "worksheets" in a single catalog, and search across all of them.

Paper forms and lab notebooks

Paper notebooks and forms are where a lot of experimental data is currently recorded - results of particular experiments, details of methods and protocols. But there is a disconnect between paper and the files where the data is stored - writing down filenames can be error prone, and it's hard to find the relevant page of a lab book while you're looking at data on the computer.

With Catalyzer it is possible to set up slick data entry forms (with push buttons and menus) to record structured information directly into the computer - so there's no need to enter it twice.

Using Catalyzer as an electronic lab notebook, you can link directly to data files, and have all the benefits of search ... and built-in web publishing too.

Databases

Some people set up their own relational databases to store their information, using tools like Access and Filemaker. These tools are significantly harder to use than spreadsheets and word processors, particularly when you have many types of complex structured information, and you usually need a database programmer to set one up. Relational databases weren't designed to cope with hierarchical structures like the file system either and tend to be quite inflexible in terms of changing structures - they optimise for search speed rather than flexibility.

With Catalyzer, you get the benefits of structured data and powerful search associated with databases, but the simplicity of tools like spreadsheets and word processors - you don't need to be a programmer to use Catalyzer. Catalyzer can also be used as a curation and submission tool for entering structured information into databases - it saves catalogs in standard XML format, which makes integration straightforward (XML is a generalisation of the HTML format used in the web).

The key benefits of using Catalyzer are:

• Gathering well-structured information at source.
• You can set up your own custom forms to gather data.
• Adding custom annotation to files.
• Adding links between different files and records.
• Automatic generation of well structured websites.
• Powerful searching and browsing.
• Automatic thumbnailing of images and other data types.
• Auto-extraction of header information from scientific file formats.

Catalyzer can be used in many different ways; the following sections outline some possibilities - as a complement to spreadsheets; for file / image archiving, for web publishing. Visit the website www.axiope.com for more examples.

An alternative / complement to spreadsheets

Spreadsheets are fine for small amounts of tabular data - but if you have lots of spreadsheet files, or you'd like to add cross links between worksheets, or you'd like to sift out particular subsets of data from multiple spreadsheets, or you'd like to publish a web database with information in the spreadsheet, Catalyzer is a lot more convenient.

You can highlight tables in the spreadsheet, and simply copy and paste them into Catalzyer. Catalyzer builds in a spreadsheet-like view, so you can edit data in a familiar tabular fashion. The power of Catalyzer is that you can have multiple tables arranged into folders / subfolders - combining the familiar benefits of the file system with tabular data. Other benefits of using Catalyzer include: built in web publishing, ability to search across all the data and better handling of links to data files / images.

Archiving data on CDs / DVDs

Many groups generate large amounts of data, which they store on CDs or DVDs. The problem here is keeping track of all the data (which CD was that file on?) when the volume of data is too great to store it all on hard disk.

The Catalyzer solution is to create a catalog of each CD - you can do this by importing all the files. You can then add notes or annotations at the top level folder, perhaps a "CD Label", "Shelf number" and "Room number" so that when you search the catalog you'll be able to find the CD.

For all types of files, the catalog will contain basic information such as the filename, modification date and folder. For images, and data files for which an importer is available, the catalog will also contain thumbnail images. The advantage of creating catalogs is that the catalog files are very small compared to the total data size - so you can keep all the catalog files on hard disk even though the data is on CDs on the shelf. You can also search across catalogs (including by thuumbnail).

You can also create structured websites of your catalogs, so you can browse the thumbnails and the filename information to find which CD has the data you're looking for.

Currently there is a limit to the total number of records which can be stored in an individual catalog (of around 10,000 records), so you might choose to have one catalog for each experiment, but you can have as many catalogs as you like. Future versions of the Catalyzer Workgroup Server will allow seamless searching, browsing and merging across thousands of catalogs.

An electronic lab book

Many people find Catalyzer is flexible enough to use as an electronic lab book - recording experimental data directly into the computer at source (rather than writing down on paper and typing into a computer later).

The way this works is to set up structures - using folders and subfolders - and then set up the data entry form for each experiment. For example, you could make a form for a "Recording" with fields "date", "notes", "strain", "result", "link to data file", "link to protocol". Where entries have a restricted set of possibilities (e.g. a result could be "good" or "bad", a strain could be chosen from 10 different options), you can set up menus and choice buttons to make it simpler to enter information.

Catalyzer then gives you a customizable form for recording your information the way you choose. Once the information is in a catalog, you have access to all the standard search and browse features, and you can link directly to any associated data files rather than having to write down long filenames by hand. You can also include thumbnails of graphs or images, link directly to spreadsheets or data files, and build up a complete record of all the information relevant to the experiment. Of course most people will use an electronic lab notebook as complementary to their paper one rather than a replacement, for use with more structured data collection.

Creating web databases to share information

Many groups have important information which needs to be shared - such as details of stocks, samples, protocols, or contact details and bibliography information with links to PDF papers.

Web publishing is built into Catalyzer - once you have the information in a catalog, you can press a button and you have a website. So making a web database of stocks available to everyone in the group, which perhaps you currently have in a spreadsheet is simply a matter of copying / pasting the tables into Catalyzer and pressing Publish. It is also simple to migrate data from relational databases into Catalyzer for its superior flexibility and simplicity, either by exporting (in "CSV" format), or using the database import plugin.

A catalog is a self-contained file in which you can store a hierarchy of records. You can have multiple different types or "classes" of records in the catalog, which store different types of information.

You can copy a spreadsheet table into a catalog - each row becomes a record, and the set of column headings defines a new class of data. You can import a folder of data files into a catalog - you get a record for each data file and folder, with links pointing at the actual data, and thumbnails for images. You can create your own classes of information in a catalog - essentially setting up your own data entry forms with menus and buttons for gathering structured information. You can add in the links between different records - e.g. to connect the data files to analysis files, or to documents detailing exact versions of protocols used.

The unique feature of catalyzer is that it will cope with any mix of information - links to data files, information from spreadsheets and databases. It is also simple enough for anyone to be able to set up and use - you don't have to be a programmer. But programmers like Catalyzer too - as Catalogs are saved in a standard format ("XML"), they are simple to integrate with existing systems and databases.

Catalog files

Catalogs are simply saved as files, which you can move around on your file system and email as attachments just as you can with spreadsheets or documents. In this respect a catalog is more like a document than a database.

Many people use catalogs to add extra information about data files on disk (beyond what is coded in the filename). In this case it makes sense to structure the catalog to echo the structure of the file system - using the same folders / subfolders.

Structure of files on file system

data/ papers/ paper1.pdf protocol/ prot1.doc expts/ jan/ image1.jpg image2.jpg feb/ image1.jpg image2.jpg

Catalyzer catalog of data

You can also add extra annotation and links to the basic catalog. For example you could add a "notes" field to the folder for each batch of data; or you could add extra menu choices to each individual data file to record information such as "strain", "protocol". You could add link from each paper to all the analysis and raw data files which it was based on.

Catalyzer catalog of data with extra annotations

The section on creating classes describes how to add your own annotation fields.

Spreadsheets are fine for managing individual worksheets of data, but they are not so suitable when it comes to managing large numbers of worksheets, or complex connections between worksheets.

You can use a catalog as a place to store and structure tabular data from spreadsheets.

For example, you may have a number of spreadsheets like:-

data-jan-5.xls:-

name strain result quality notes r1 a100 56 ok r2 a100 72 med r3 a200 76 bad some noise r4 a200 30 ok r5 a200 22 ok

and strain-info.xls:-

strain sample-room freezer desc a100 100 G knockout of XYZ a200 76 H wild type

and store all your spreadsheets in a directory like:

strains/ strain-info.xls jan/ data-jan-5.xls data-jan-7.xls data-jan-8.xls data-jan-9.xls data-jan-10.xls

The problem then becomes - how to sift out data which is scattered across multiple spreadsheets? (e.g. to choose all the good quality data values for a particular strain). With the spreadsheet you have to resort to time consuming manual copy / paste of rows to extract the data you want.

If you copy the data into Catalyzer, however, you can do instant sorting and searching across all the data.

You could structure the catalog similarly to the file system: and then copy each spreadsheet into a different folder of the catalog.

Catalyzer viewing a single worksheet from a spreadsheet

Once you have the data as a catalog, you are free to:

• - Search and browse across all the spreadsheets at once, so you could extract all the good results sorted by strain
• - Link together the different types of data - e.g. making a direct connection from the strain name in the results field to the data from the strain-infor spreadsheet
• - Publish the catalog as a website to make it easy for anyone in the group to browse.

Combining data from multiple spreadsheets, and pulling out all the 'bad' quality rows

A simpler database

Because catalogs are based around familiar notions of folders and subfolders, they are often easier to use than database applications, which typically need a programmer to set up.

You can set up a catalog to store the types of information you may have put in a database before Catalyzer was available.

There are a number of ways of automatically importing the data you have in a database into a catalog (see section importing data from a database).

You could set up a catalog to record data directly as you gather it - so it's already structured and in the computer, and you don't need to type information from paper notes. An example catalog structure could be:

Using Catalyzer as an electronic lab book

One advantage of using Catalyzer (over paper and spreadsheets) is that you can make links from your notes directly to data and analysis files, and start to build up forms for the data you need to gather for each experiment.

Catalogs are flexible enough that they can contain information extracted from files and folders linked to information from spreadsheets and databases linked to custom records from your electronic notebook, all in one place.

A catalog stores information in a number of records, each of which has a name and a single class , which is the type of the record. The distinction between a Record and its Class is an important one to grasp to make best use of Catalyzer. An example of a class would be "Image" which has fields "filename", "height", "width" and "comment". An example record of class "Image" would be a particular instance - e.g. having filename "image1.jpg", height "1200", width "1600", and comment "picture of a tree".

Catalyzer lets you create your own classes to store your information, so if you wanted to store details of several Protocols, you could create a new class for "Protocol" with fields "name", "date", "researcher", "link to document", "description". You could then create several records of class Protocol, with the fields filled out for the specific protocols you wanted to record. The quick start example gives a step by step guide to using Catalyzer to create a number of different classes, and making records containing the actual information.

The importers for particular data file formats create their own classes for you automatically with fields appropriate to that format; for example, the TIFF image importer creates a class with the fields particular to TIFF images. The section on cataloging files has more details.

Examples of records and classes

Example definition of class "Protocol". This defines five fields:

Protocol: name date reseacher link to document description

protocol1: name protocol 1 date 1/1/2001 researcher Sue link to document c:\docs\prot1.doc description mix A with B and cook at temperature 95C protocol2: name protocol 2 date 09/08/2004 researcher Bob link to document c:\docs\prot2.doc description shake very hard at 27C

How Catalyzer Classes relate to tables in spreadsheets

Most people are already familiar with the underlying concepts of "records" or "classes" even if the terms are new. For example, suppose you have a table in a spreadsheet like:

number strain date result quality comment 1 a100 jan 121 good ok 2 s101 feb 121 bad hmmn

Another example of class and records - Samples

Example class definition for a database of samples:

Sample: id name quantity freezer location

sample1: id 1001 name sample1 quantity 100g freezer location G sample7: id 2007 name sample7 quantity 10kg freezer location H7

Defining the Sample class using Catalyzer. A number of fields have been added (id, freezer location, etc). In addition, the 'room name' field has been changed to have the field type 'radio buttons', with three preset values.

Editing the values of a Sample record. Most fields allow text entry, but the 'room name' field lets you enter data but clicking on a button.

Folders

You can arrange records in a catalog in a hierarchy of folders, just as you can arrange files in subdirectories on disk. Each folder can contain a list of records of different types or "classes". When you first open a catalog, it has a single root folder (initially called "untitled"). You can add subfolders to this (right-click on the folder (ctrl-click on Mac), select Add Using Class : Folder). You can also add any other type of record e.g. using Add Using Class : Protocol.

So you can organise your catalogs as you like. For example you might set up a folder hierarchy like:

mycatalog/ pictures/ jan/ feb/ graphs/ excel/ analyses/ samples/ publications/ nature/ science/

Although the "Folder" class is built in when you start up Catalyzer, it is just a regular class with a single field "Contents" which can contain a list of records. So you can add sublists to your own classes, and then add subrecords to them.

Field types

You can assign a field type to a field - so you can specify that certain fields should only contain a date, a number, or should be chosen from a menu. For menu fields, you can edit the different menu options as you go. The 'room name' field in the Sample class above had a type set to be 'Radio Buttons' to make it quicker to enter data.

You can edit the classes to reflect the type of data that you want to store in your catalog. You can add fields for different purposes, for example menus, radio buttons, check boxes or links to websites and data files.

If you apply a change to a class in a catalog, then that change automatically applies to all records using that class. For example, if you add a "notes" field to an "Image" class, then all your Image records will have a slot for you to add notes.

Technical note: If you are familiar with relational databases (like Access, Filemaker, Oracle), then a class corresponds roughly to a table definition, but the data model of Catalyzer is more flexible than relational databases, as you can add different classes of record anywhere in the folder hierarchy. It is possible to import the contents and structure of a relational database into Catalyzer using the Database importer.

Once you have defined a new class, you can start to add Records of that class to particular folders in the catalog.

Creating Records

A record is a set of values entered in the fields of a class; it is an actual instance of its class. You put a value in for each field. For example, in a field called `Name', you enter the name of a person, in a field called "notes" you might enter some longer text. The class defines the structure of a record. Each record has a single associated class which defines which fields must be filled in. A class may have many different records which use it.

Records live in the hierarchical tree structure of the catalog - so you can have records with lists of subrecords, just as you can have nested folders in the file system. You can create a hierarchy of records by adding Folders and sub folders. You can then add records to any folder.

Catalyzer makes it easy to switch between data entry mode (adding and editing records) and class editing mode (adding fields to classes and making new classes). (see the Creating Catalogs section for which buttons to press; the switch is available from the main menu View : Catalog to enter data, and View : Class to edit class structure.) This means that it is not essential to get the design of the class perfect first time - you can start off thinking, for example, that to describe an Experiment you only need to record the date, the sample and some notes. As you add more Experiment records, you realise it would also be useful to record the temperature and results - so you can switch into class editing mode and add these extra fields to record temperature and results.

One application of Catalyzer is to combine data from multiple sources - in one catalog you can have many different spreadsheet tables, the contents of a Samples database, links to data files and documents, with associated custom annotation.

This chapter explains how to enter your data in Catalyzer by creating catalogs, classes and records. The catalog, class and record system in Catalyzer lets you organize information into a hierarchical tree structure. (see the Introduction to Records and Classes in the previous section for an explanation of these terms). This chapter covers the following topics:

• Starting to use Catalyzer. This section describes how to make a new catalog, and explains the toolbar and keyboard shortcuts.
• Catalog editing modes : Catalog Window and Class Window. This section describes how to switch between the two editing modes of Catalyzer - Catalog editing, and Class editing.
• Loading and Saving Catalogs. This section describes how to load and save catalog files, and how to open up the built in examples.
• Adding Records. Catalogs store a hierarchy of records of information; this sections shows how to add, delete, rename and duplicate records and folders. Each record must have an associated class which defines its fields - so you may want to read this section along with the one on Creating Classes.
• Editing Records is very simple in Catalyzer, as you just need to fill in a form defined by the record's class.
• Creating Classes shows how to create your own classes, with your own set of fields.

Shortcuts

If you want to create a catalog of data you already have on CD or hard disk, you may wish to skip to Cataloging files on hard disk / CD If you want to convert data you have in a spreadsheet, skip to Importing Spreadsheets using copy/paste.

Key features

The quick start tutorial on Creating a Catalog from Scratch should be useful in covering the main Catalyzer features in a short time.

It is particularly important to get familiar with the two modes of Catalyzer - Catalog Editing Mode, and Class Editing mode. These are described in the Catalogs Editing Modes section below.

When you first start Catalyzer, you will see the Quick Start screen, outlined in the first section. This presents a number of common start points for creating a catalog, including creating a new catalog, and creating catalog of data you already have on your hard disk.

Creating a new empty catalog from the main menu

Creating a new empty catalog from the toolbar

The first time you run Catalyzer it will operate in Lite Mode. This lets you edit and save small catalogs. For full functionality you need a license, available from Axiope. See Licensing Catalyzer and Plugins for details.

The figure below shows the main catalog window:

Catalog Window with empty catalog

The second row in the image is the main toolbar. It has buttons for the following functions:
New Catalog creates a new catalog
Quickstart launches the Quickstart window
Open Catalog displays a file browser for you to browse to a catalog and open it
Save Catalog saves the currently opened catalog
Undo undoes the last thing you did
Redo cancels the last undo
Previous views the previous record in a list
Next views the next record in a list
Catalog Window displays the Catalog window
Class Window displays the Class window

The main area is the Record panel. This displays the values in the selected record.

To the left of the window is the Catalog tree panel. This displays the record hierarchy in a tree view. Use this panel to select a record to display in the Class/Record panel. You can add, delete, duplicate and change the order of records using the buttons at the top of this panel.

Navigating in Catalyzer

The toolbar gives you access to the main features in Catalyzer. You can also use the File menu to open and save catalogs. Use the Catalog Window and Class Window buttons to display the main editing windows. See the next section, Creating Catalogs for more information on the Class window.

Keyboard shortcuts

You can also use keyboard navigation to move around in Catalyzer. The most important keyboard shortcuts are:

• TAB: use this key to take you to the next field
• RETURN: use this key to add options to a list, and to select or deselect checkboxes. You can also use this key to add fields to a class.
• CTRL-C and CTRL-V (Windows, Linux) or Command-C and Command-V (Mac OS): use these keys to copy and paste items
• ARROW keys: use these to move around in a list or table.

There are shortcuts for most functions that are available from menus in Catalyzer. The shortcut is indicated to the right of the item's name in the menu. For example, the first item in the File menu is New, and its keyboard shortcut is shown as "CTRL-N".

The Catalog window and Class window

Catalyzer has two editing modes - Catalog Window and Class Window. Most of the time you use the Catalog Window, which lets you edit the content of a catalog - typing values into fields, and adding records. The Class Window is used for editing the structure of a catalog - adding new classes, and adding/removing fields from classes.

See the section Records and Classes for a definition of the difference between records and classes.

You can switch between the two modes using the toolbar:

Select the Catalog Window to edit catalog content

Select the Class Window to edit catalog structure

Select the Catalog Window to edit catalog content

Select the Class Window to edit catalog structure

Catalog Window - for editing catalog content. A record of class 'Photo' is displayed.

Class Window - for editing catalog structure. This example shows how one could edit the 'Photo' class by editing the fields - in this example the 'Image' field is highlighted.

The left panel displays an expandable tree view of the catalog, showing the records within it. If a record has a folder icon, this means it may contain one or more sub-records. You can expand these records to view the sub-records.

Each record has a name displayed in the tree view. Select a record in the tree view to display the contents in the right panel. You can rename a record by double-clicking on its name in the tree.

Loading Catalogs

You can load catalogs using the toolbar:

Load a catalog using the toolbar button

Loading a catalog using the main menu

Loading an example catalog

Loading an example catalog

A number of example catalogs are bundled with Catalyzer. You can load them from the Help menu.

Saving Catalogs

Save a catalog using the toolbar button

To save a catalog, click the Save button on the toolbar, or choose File > Save from the main menu.

The default file extension for Catalyzer catalogs is .axz. This file contains both the catalog, and its type catalog (with the classes).

To add a record, right-click (ctrl-click on Mac) on a folder in the catalog, and select: Add Using Class. The menu displays all the types of record available - initially the choices are "Folder", "Record", and "New Class...".

There is a section of the Quick Start guide on Creating a Catalog from Scratch which includes step by step instructions on adding records. When you first start using Catalyzer, you may find it helpful to load up an example catalog to experiment with the controls. (Help : Examples from the main menu).

Adding a new record

Adding a new Folder record to a catalog

You can add a record from the Catalog tree panel to a Folder. To add a record in this way, right-click (ctrl-click on Mac) on the catalog in tree view and select Add or Add using Class: You can also click the Add button on the toolbar.

When you first start Catalyzer, the only classes available are "Folder" and "Record". So you can Add Using Class : Folder to make your folder hierarchy, and Add Using Class : Record to add empty records - but to actually start entering any information into the catalog, you need to add some of your own classes and fields. The Add Using Class : New Class... option (described below) is a start; but see also the section on Creating Classes to find out how to add fields to classes.

One quick way of creating a catalog is to import data from the file system. The file importers create classes for you automatically, and also create a record for each file on disk. See the section on cataloging files for details.

Renaming a record

Renaming a Folder record

You can rename a record by double-clicking on the record's name in the tree view and editing the text. A "Rename" menu option is also available by right-clicking records in the catalog tree view (ctrl-click on Mac). If one of the fields has been designated as the record's name (see note below for how to do this), then you have to edit that field's value to set the name instead of editing it in the tree view.

It is also possible to choose one of the record's fields as its name. To do this, the class defines where the name of a record comes from. For any class, you can designate a particular field as being used to give a name to records of that class: in the Class Window, right-click on a field name and select Set as Name from the menu. The icon appears next to the field name, to show which field is used as the record's name. The Set as Name menu option acts as a toggle, so you can also unset the choice of field to use as the name.

Duplicating a record

The duplicate button on the toolbar duplicates a record. This can be a useful way of adding several records with similar content.

Duplicating record

Adding new class of record

Initially the only classes of record available are "Folder" and "Record". You can add a record of a new class using the "Add Using : New Class..." menu:

Adding a new class of record

Creating a 'Person' record

The new record will have no fields until you add them; see the adding fields section to find out how to do this.

Viewing a record

To display a particular record, click on its name in the tree view. The corresponding record will be highlighted and displayed in the main window.

Editing a record

To begin editing a record, select it in the catalog tree view. The record displays in the Class/Record panel and you can begin adding and editing values.

Moving and copying records

You can move or copy records using cut and paste. To cut a record to the clipboard, right-click and choose Cut from the pop-up menu (CTRL-X on Windows and Linux, Command-X on Mac OS). The record will be moved from the catalog onto the clipboard. You can now paste the record somewhere else in the catalog by selecting the destination record and choosing Paste from the right-click menu (CTRL-V on Windows and Linux, Command-V on Mac). To copy the record to the clipboard without removing the original, use Copy (CTRL-C on Windows and Linux, Command-C on Mac OS) instead of Cut.

On Windows, you can also move or copy records by dragging them in the catalog tree view. To move a record, drag it onto any other record which accepts children. Records which can accept children are displayed with a folder icon. If you hold down the CTRL key while dragging, the record will be copied rather than moved.

You can move or copy several records at once. Select a record in the catalog tree view as normal, then hold down shift and select another record. These records and all intervening records will be selected. Now drag, cut or copy the records as described above.

If you press the Add button on the toolbar, it will add another record of the same class as the last record you added. As a short cut to add a particular class of record, you can also right-click (ctrl-click on Mac) on the Add button to popup a menu.

The Folder class which is included when you start Catalyzer is just a regular class - which has a "Contents" field which can contain a list of records. So you can add a subfolder by adding a record of class "Folder". You can also extend the Folder class to add your own fields (e.g. "notes"). This can be used to annotate a entire folder of records. And you can create your own custom Folder classes by duplicating the Folder class and adding extra fields - or by adding a record list field to any class.

If there is an information icon, , beside a field then there are guidelines for entering information in that field. The information displays as a tool tip window when you hover over the icon. You can also right-click on the to display the help text in a pop-up window.

This tool tip text only appears if the user that created the class filled out the Help text field option. For more information on adding help text to a field, see Using the field options.

Once you've added a record, you can edit its values in the main window. There are a number of different types of field, including text entries, radio buttons, menus and dates.

Editing a single record

You need to be in Catalog editing mode and have a particular record selected to edit values of a record. See the section on Catalog and Class mode for how to switch to Catalog editing mode (hint: View : Catalog).

Classes determine what information you can enter by providing a list of fields. An Image class may have fields for name, size and creation date for example. These fields would require a piece of text for the name field, a number for the size field and a date for the creation date field.

The power of Catalyzer is that you can create and modify your own classes to fit your needs - so you could make classes for Protocols, Specimens, Experiments, Publications, Analyses and customise them for your situation.

Using the Class window

Select the Class Window to edit the types or 'classes' of record you can add to a catalog

To create, modify or delete classes, click the Class Window button (or View > Class from the main menu). This puts Catalyzer in class editing mode and you can now add and edit classes and fields. (the other mode is Catalog editing mode for data entry).

The Class Window editing a class. The '+' button in the middle toolbar lets you add a new field to any class. You can rename the field using the panel on the right.

The Class Window after adding and renaming three fields.

The left panel displays an expandable tree view of the catalog, showing the records within it. Underneath, at the bottom left panel of the window is a list of all the classes in the catalog.

Adding, removing and renaming classes

The Classes toolbar includes buttons to Add, Remove, and Duplicate classes.

Classes can be renamed by double-clicking on the name in the list of classes. Alternatively, this can be done using the context sensitive menu (usually right-click on the class name) (right-click>Rename).

Each record has an associated class. Selecting either a record or a class brings up the appropriate class in the middle panel. Each class comprises a number of fields. The attributes of the selected field are shown in the panel on the right.

Selecting a field to edit

To select a field, click on its name. This highlights the field and its details are shown on the right hand side. In the example above, the sample field is selected, and the field attribute panel shows that the name of the field is "sample", and its field type is "Text" (a link to a file or URL).

The details for the field are shown in the rightmost pane. Here you can change the field name and the field type (for example, Text, Date, Menu). You can also add help text for the field, to guide people entering information.

Right-click (ctrl-click on Mac) on the field name to popup a context menu - this includes options to add, remove and duplicate fields.

Adding a record of the new class

For adding and editing records after you've been editing classes, switch back to Catalog editing mode (View : Catalog from the main menu).

When you first create a class, you won't be able to type in any values in the fields. To do this, you need to add a record of the class to the catalog. You can do this by right-clicking on a folder of the catalog (ctrl-click on Mac), and selecting Add Using Class : MyNewClass. The section on Adding Records has more detail.

To add new fields to a class, make sure you're in class editing mode ( Class Window button on toolbar).

Select the record or class you want to add the field to. Click the Add Field button in the center Class/Record panel.

Adding a field to a class

The field is initially given a name like "Field 2" - to give it a sensible name, edit the Field Name entry in the rightmost panel of the screen.

The right hand panel contains details for the new field

You can also specify a Field Type. Initially, all fields have the type Text - this is a single line text entry field. Other field types include Menu, multi-line Text Box, Date, Time, Number, Color, Checkbox, Choice, Radio Buttons.

Changing the field type to a Radio button

Entering values for the Radio button

A new Quality field has been added to the Photo class

The List field type lets you create sublists of records and other types, and is the key to creating hierarchical structure in a catalog.

The Record field type lets you add subrecords - for example, the Photo class in the example mountains catalog has an exposure subrecord to hold the exposure settings.

The Reference field type lets you create pointers to other records in the catalog. This is useful for cases where a number of records refer to some common data. For example, you could create a number of Protocol records, and each Experiment could contain a reference field which points at its Protocol. Clicking on a reference field entry brings up a dialog for selecting the target of the reference. In the website view of a catalog, the references become hyperlinks - and it also displays all the records which refer to the current record (for example, when browsing to a Protocol it shows a list of the Experiments which used it).

The Resource field type lets you add URL links to websites or data files.

Deleting a field

You can remove a field by right-clicking on it and selecting Remove, or you can use the Remove button on the middle panel toolbar.

Keyboard shortcut: To delete a field or an item, you can select it and click the DELETE key.

Duplicating a field

You can duplcate a field by right-clicking on it (ctrl-click on Mac) and selecting Duplicate, or you can use the Duplicate button on the middle panel toolbar.

You can change the name and type of the field by using the options in the Field Options panel on the right. All the fields have these common options listed below. The next chapter, Making Classes Classy describes the different types of field available in more detail.

The field panel on the right lets you change field name and type, as well as (optionally) add help text and color.

Field Name	This lets you give your field a name, for example if you want the field to display the name of a region, you can call it a `Region'.
Field Type	This indicates what type of information you can enter in the field. Allowed types include Text, Text Box, Menu and Number. A full list of the available types is provided in the next section.
Help	This text box lets you enter information about the field, for example what the purpose of the field is, or what type of value a user can enter. This information is displayed as a pop-up tool tip when the user places the mouse over the information icon next to the field.
Color	This field lets you color code the background of a field, for example if you want to make mandatory fields red.

Adding field types

The following field types are available for you to add to a class:

The previous chapter showed how to create classes and records. This one shows how to make it simple to add different types of information to a record - using menus, links to data files, and references.

A comprehensive list of types is included in the Reference of field types chapter; this chapter introduces what is available.

A number of different field types are available - this page shows examples of text, menus, numbers, dates and times. The next page shows how to add subrecords and lists to add more complex structure to your catalogs. Being able to represent links and cross references to other items of data is a key advantage of Catalyzer, and the pages on References to other records in the catalog and Resources - other files show how. The previous chapter showed how to add a field and change its type using the "Field type" selector.

The default type of field "Text" gives you single line text entry:

A "text box" lets you enter a paragraph of information:

You can copy and paste information from other applications using ctrl-C and ctrl-V (command-C and command-V on Mac).

See also the reference pages on adding Text and Text Box fields.

There are a number of other types available to you to make it simpler to enter data:

Menus, choices, checkboxes and buttons

You can construct your own menus with your own options:

These can contain subitems, and you can edit them to contain your own items.

Checkboxes let you signal a yes/no value:

Choices are similar to menus, but you can select multiple values:

Radio buttons are another way to display menu options:

If you convert a "Text" field type to a "Menu" type, the menu will automatically be populated with all the different values the text field contains.

See also the reference pages on adding Menu, Choice and Radio fields.

Numbers, dates and times

For numerical values, you can use the Number type:

The date field lets you add dates:

It's also possible to store an empty value in a field - right-click on the field name and choose "Remove value".

See also the reference pages on adding Number, Date and Time fields.

As well as simple text and menus, you can store lists of other records in a field - e.g. you could add a field to an "Experiment" record to hold a list of "Results" or "Analyses".

The "Folder" class has a field called "Contents" which contains a list of other records:

Viewing a list of records

Adding a record to a list

You can add items to the list with the "+" button on the bottom left, and there's a right-click menu (ctrl-click on Mac) for deleting items and reordering them.

Expanding a list in 'spreadsheet mode'

Press the small button on the bottom right to expand out the list contents as a spreadsheet-like table view:

Viewing the contents of a list as a Table

Full screen spreadsheet mode

Click on the "Expanded Table View" button to fill the window:

Click the Expanded Table button to make the list fill the window

The expanded table view

See also the reference pages on adding List fields.

Adding structure : subrecords

You an set a field type to hold a single "Record". This allows you to add a subrecord:

Clicking on the "+" icon expands the subrecord in place:

See also the reference pages on adding Record fields.

You can include references to other records in the catalog. The field type is "Reference". This is useful if multiple records want to refer to the same piece of information (e.g. many experiments may use the same sample).

Adding links : references to other records within a catalog

A reference to another record shows the target record's name:

Click on the "+" button to expand the target record:

The Folder icon lets you point the reference at a new record; the arrow jumps to that record.

Reference or Subrecord?

A reference field looks similar to a Subrecord field - which should I use? The rule here is that a reference is used when you're pointing to a record which is already stored somewhere else in the catalog. You can have multiple references to the same record. A Subrecord field is useful when a record is only used by its parent.

Reverse Links: When you publish a catalog as a website, you'll see the references as hyperlinks - but you'll also see a list of all records which reference a particular record - so when you browse to the Protocol, you'll see a list of all corresponding Experiment records.

See also the reference pages on adding Reference fields.

Another very useful field type is the "Resource". This can be a link to a file on disk, or a weblink.

If you include a link to a file in a catalog, the file itself is not stored with the catalog - just the link.

What if I move the file? You can fix up broken links using the Resource link dialog. This allows you to change the path if you move the data from one disk to another, or to a network drive. The menu option is Edit : Resources..., and the dialog is described in the section on the Find Resources Dialog

How do I view the file? Click the Preview button to the right of the resource.

How do I link to web databases? You can use a resource field to store a URL (just copy / paste the http:// address from your web browser).

What if the file is on CD, not on hard disk? You can use catalogs to search and browse for data even if the data files are on a CD on a shelf. To access the file itself you'll need to slot in the CD, but the catalog contains enough information (and thumbnails) to let you find the CD to insert.

See also the reference pages on adding Resource fields.

Catalyzer includes spreadsheet-like features for editing tables of information within the program.

Note also that it is also very simple to copy data from Catalyzer into a spreadsheet (from the browse or search windows) - and from a spreadsheet back to Catalyzer ("import spreadsheet").

See also the earlier section on cataloging multiple spreadsheets and List Fields.

You can view any list of records in "spreadsheet mode" - just press the "Table View" button in the scrollbar.

Click the 'Table View' button to view any list in spreadsheet mode

Spreadsheet mode. The 'List View' button switches back to simple list mode

The editing in this mode is similar, but not identical to spreadsheets. Some differences:

• - Rows for records and fields which actually exist are shown with a white background; where there isn't yet any data, it is shown with a grey background.
• - The column headers show the field names. In a spreadsheet they typically show the labels "A B C" etc. In Catalyzer you can rename a field by double-clicking on a column header.
• - In a spreadsheet you are free to put any information anywhere. A Catalyzer table is more structured; a single table can only contain rows of a single Class.

A number of features are the same as with spreadsheets:

• - You can just type a value into any square.
• - You can highlight an area and copy / paste.
• - You can scroll down / right to infinity.
• - You can have multiple "worksheets" in a list. In Catalyzer, you use a different "worksheet" for each different class of record (e.g. "Image", "Paper"). Remember, a class of record corresponds to a particular set of column headers / field names.

Creating a new table from scratch

This section describes how to create a new table in Catalyzer. It will be used to hold 'Sample' records, and have the column headers 'name', 'location', 'date', 'desc'.

Start with an empty catalog File : New Right-click on the root folder (ctrl-click on Mac), Add Using Class : New Class... Click on the 'New Folder' checkbox. For 'Folder class' pick 'New Class', for the new class name type 'Sample'. You should see a new folder in the catalog called 'Sample List'. Add a sample to the list Add Using Class : Sample. Switch to table mode (the Table View button on the bottom right). Add a Sample record to the folder (Add Using Class : Sample). Now you can treat the table of samples similarly to a spreadsheet: type values into any empty cell, double-click on column headers to rename them, and copy/paste between areas of the cell.

Click the Table View button to switch into table mode

The Add Item button adds new rows to the table

You can enter values for the cells in similar manner to a spreadsheet. Double-click on the column headers to rename the columns.

Adding records in table mode

To add a record to a list, simply start typing in an empty cell, as you would in a spreadsheet to add a new row.

There is also the standard menu available from the ">>" icon, which lets you add a record of a given class, or of a new class.

Catalyzer equivalent of "Add Worksheet"

There are two ways to add a new 'Worksheet' table. You can add a new Folder to the catalog, and edit it as a table. Or you can add records of a different class to a single list; the different classes will be displayed in different tables. The equivalent to "Add worksheet" in a spreadsheet is to add a Folder (using right-click/ctrl-click on the "+" button, or left-click on the ">>" menu button.

Renaming column headers

You can rename a column header by double-clicking on the header.

Setting the type of a field

Right-click (ctrl-click on Mac) on the header, and select the "Attributes". A new window will appear which lets you set the name, type and help text of the field.

The "(any)" tab

If your list contains different types / classes of record, there will be one tab for each class (e.g. "Image", "Experiment"), and an extra tab called "(any)". This lists the names and classes of all records in the list - but you can't edit field values in this mode. Editing only works when you're only viewing records of a single class (click on a tab, e.g. "Image", or use the right-click/ctrl-click menu option: Show class :.

Full size table mode

The "<>" button at the bottom right of a list expands a list into "full window" mode. (The "><" button toggles back again). This gives you maximum screen space for editing a table of information.

Expanded table view

It is possible to import tabular data directly from spreadsheets and databases. This can either be done using copy / paste (highlight the table in the spreadsheet, copy it to the clipboard (using CTRL-C or Command-C on Mac), then paste it into a folder of Catalyzer (right-click>Import>Clipboard on a folder in the catalog tree). You can also import data files in CSV format, a standard interchange format for spreadsheets (right-click>Import>File on a folder in the catalog tree, and pick a .csv file) - see the next page for more details.

Catalyzer assumes the first row of the table holds the field names and subsequent rows each hold a single data entry, for example:

Example of Spreadsheet Data Format

Copying data from Excel

Pasting clipboard data into Catalyzer

The data pasted into Catalyzer (click the Table View button at the bottom right to get this view)

An individual record viewed in Catalyzer. Note that the field names correspond to the column headers in the spreadsheet.

Switching to Class view to rename the Imported Entry class as Person.

To export data back to a spreadsheet, use the Copy button in the "Browse view" or the "Search results"

If you save spreadsheets in "CSV Format", you can import them into Catalyzer. This is an alternative to the Copy/Paste method described in the previous section.

Saving a spreadsheet in CSV format. All spreadsheet applications have an option to save data in the standard CSV format (it will appear in the Save or Export menu on the spreadsheet application). Note that Catalyzer does not yet have a plug-in that can read the native file formats of spreadsheets (like .xls for Excel). If your spreadsheet application prompts you to choose a character to use for the quotation marks and field separator, choose quote marks and commas respectively.

Save a spreadsheet table in CSV format. Saving a spreadsheet in CSV format. Most spreadsheet applications include an option to save as CSV. Start Catalyzer and create a new Catalog (File > New Catalog): Right-click (CTRL-click on Mac) on the root folder (called untitled at the start) and select Import > File... from the pop-up menu to import all the data in the file, as shown in the following screen: Importing File You can import CSV files anywhere in an existing catalog, so you can import multiple spreadsheets into a single catalog. The following screen is displayed when you select Import > File: Import File Dialog Type the address of the file or click Browse to browse to the file you want to import, select it and click Open. The .csv file has been imported into your catalog. Select your catalog in the tree view; a new record is there for each line of the spreadsheet, for example: Each row of the CSV file becomes a record. You can also import other catalogs in this way, as well as other file formats - Import>File and browse to a catalog (with extension .axz or .axc). If you try to import a file that Catalyzer does not recognize, it imports the header information only.

You can export tabular data from the Edit>Browse and Edit>Search panels by selecting the records to view and pressing the Copy button. This copies the table into the clipboard, so you can then open up a spreadsheet and paste the data (using CTRL-V).

Press Copy from the Browse window

Press Paste in the spreadsheet

This chapter describes the search and browse facilities in Catalyzer, which allow you to:

• Do simple text searches
• Do specific field value searches
• Browse a catalog in tree and tabular views

In the main toolbar of the catalog window is a box for typing in a search word: press the button to the right to perform the search.

Simple Search is available from the main window

Search results are grouped by class - Photo and Trip in this case

Search results are shown in a table. You can view any record in the main Catalyzer window by clicking on the row. You can also sort the search results by clicking on the column headers. If your result includes more than one type of record these will be displayed as Tabs, which you can click on to see (e.g.) just the Image records, or just the Experiment records which match.

The next section shows how to perform more complex searches, combining multiple terms.

The Search Catalog dialog is accessed from the main menu (Edit>Search). It consists of two sections. The top half lets you define the criteria of the search, the bottom half shows the results of the current search.

Start the Search dialog from the main menu

The Advanced Search window - the button on the top right toggles between simple and advanced search

The search criteria toolbar at the top has the following components:

• Add Search Filter - appends a new search filter row to the search filter table (below the toolbar).
• Duplicate Search Filters - duplicates currently selected rows in the search filter table. This is useful if the user wishes to search for a set of values in a specific class/field.
• Remove Search Filters - removes the currently selected rows in the search filter table.
• Match type - Match all means matching records must have matched all the defined filters, Match any means matching records need only match at least one of the defined filters.
• Search from - Allows the user to define the root of the search. Only the search root and any subrecords of the search root will be searched. If the 'Search from' record is the catalog root, the entire catalog will be searched.

The search filter table consists of individual search filters, added using the toolbar Add button. Each search filter has the following components:

• Filter class - for 'Field value' filters, this restricts the value search to a single record class, or '(any class)' to leave the record class unrestricted.
• Filter field - for 'Field value' filters with Filter class restricted to a single class, this criteria allows the user to restrict the value search to a single field within the record class, or '(any field)' to leave the record field unrestricted.
• Filter relation - for 'Field value' filters, this allows the user to select the matching operation between the expected value and the record field value. For example 'contains' would allow a search value 'pp' to match field data 'apple'.
• Filter value - for 'Field value' filters, the value to search for (depending on the filter relation) or '(any value)' to leave the value unrestricted. For 'Class' filters, the allows the user to select the class of records to match, or '(any class)' to leave the record class unrestricted.

Using the filter table, complex search filters can be created. For example, you could build a filter to search for all records of class 'Document' with author 'me' that are not published in 'Nature':

The dialog updates with each search criteria change to show the matching results in the catalog. The results panel consists of the following components:

• Results table - shows matching records. If the selected results are of a single class, the table will show all fields in the result records, with the addition of 'Name' for the record name, and 'Path' for the path to the record within the catalog. If the selected results contain records of different classes, only 'Name' and 'Path' are shown. As with the browse panel, clicking on a column name will order the records by that column. Selecting a record within the table will cause Catalyzer to display the record in the main window.
• Results toolbar class selector - The selection box above the results table shows the classes of the current search results. If the results are of mixed class, the user can choose the class of records to display with all fields, or '(any class)' to display the name and path of all search results.
• Results toolbar copy to clipboard button - clicking here will copy the current search results to the clipboard from which they can be pasted into other applications such as spreadsheets.
• Results toolbar print button - clicking here will allow printing of the current search results. See the section on Printing.

Catalyzer provides an alternative way of viewing the contents of a catalog. You can use the browse facility to locate records and to view a set of records within a single window, ordered by the different field values. It is very useful for filtering particular types of data in your catalog (wherever in the catalog tree they are located). You can also copy the filter results to a spreadsheet.

The browse window lets you perform complex searches on your catalog with remarkable ease - for example you can show all Images which use compound Cy5 sorted by Date with a few mouse clicks.

Browsing a catalog

The Browse window can be opened from the main Edit menu. Opening the Browse window Select Edit > Browse in the main window. The following screen is displayed: The Browse window, showing all Photo records The left panel displays a tree view similar to the view in the main Catalog window. It is different from the catalog tree as it is organized by the classes that are used in the catalog rather than the record hierarchy. The root is All Records and under this you can see all the classes that are currently in use and how many records use each one. You can now do the following: Click a class to display all the records of that class. The records are displayed in the right panel. Expand a class in the tree view to display all the fields in that class and select one of the fields to display the records that have values for that field. Expand a field in the tree view to display all the values for that field and select one of the values to display the records that have the selected value for that field. For example, select Image>quality>good to show all images classified as "good". Showing all the Good images

Viewing records

The right panel displays the records that you are currently browsing, in a table view. Each column heading is a field name and each row contains a single record. If you click on a record in the right panel, it displays in the main Catalog window.

Sorting the records

You can sort the records by field in ascending (click once) or descending (click again) order by clicking on a column heading.

The Path column in this view displays the location of the record in the catalog hierarchy.

Copying to a spreadsheet

You can copy a subselection of data to the clipboard by pressing the Copy button on the toolbar.

The copy button is at the top right of the browse window

The contents of the browse view pasted into Excel

"Show me all my good images". One use of Catalyzer is to add annotations to data files, such as images. If you've added a quality field to your images, with values (good / medium / bad), you can use the Browse panel to instantly pick out a list of the good ones. Expand the Image class, then the quality field. The next level in the hierarchy will have the different values with the number of corresponding records (for example, good (123) / medium(46) / bad(567)). Click on the good(123) value and the table view will show all the good records. You can sort by any of the other fields by clicking on the column headers, and copy the resulting table to the clipboard by pressing the copy button. Having copied the records to the clipboard you can then paste them elsewhere in the catalog or paste them into external applications such as spreadsheets.

There are several ways you can move information between Catalyzer and other systems. Some of them are built in; others require additional modules ("plugins") to be installed. This section describes the import and export in Catalyzer and its extensions; what they are and how to use them.

Catalyzer provides import and export options that:

• Generate catalogs or records from external sources of information including spreadsheets, file headers and databases.
• Export information from catalogs to external files
• Print catalogs

Catalyzer can make a catalog of files you have on hard disk, CD or a network drive. The catalog will have the same structure of folders and subfolders as you already have - and you can extend it by adding your own fields and links between parts of the catalog. The Import Data trail of the Quickstart guide includes some step by step instructions on importing data.

The catalog stores pointers to the actual data files, so will often be much smaller than the data files themselves.

In the catalog tree, select a folder in the catalog (for a new catalog the root folder is fine), raise the right-click menu, (ctrl-click on Mac) and select Import>Folder or Import>File. You can then pick a folder or file to import.

Import data from a folder using the right-click menu (ctrl-click on Mac) on the catalog

The import dialog lets you choose the folder to import.

Import data from a folder using the File:Import menu

Once you've browsed to a directory, you can set extra options. These include which file types to include / exclude, and the size of thumbnails you want if you're importing images.

Press the Import button once you've chosen the directory.

The progress dialog displays the progress importing. Importing can take a while for large numbers of files.

The catalog which is generated by importing data has the same structure of folders as the original files. There is one record for each file and folder, with links back to the original file (in the "URL" field). Note that Catalyzer automatically creates the new classes for you to hold this information (e.g. an "Image" class for images, a "File" class for vanilla files. But you can add your own fields to these classes as you need.

The catalog which has been generated by importing files. Note that Catalyzer spots the images and makes thumbnails of them.

Catalyzer is able to make "thumbnails" (small versions of an image) for many image formats - including JPEG, TIFF, PNG, BMP.

Check the 'Thumbnails' box on a Resource field to make thumbnails

How do I change the size of the thumbnails?

Thumbnail size is set when you do an Import. The dialog includes options (small, medium, large), and additionally some import modules include some custom settings to control thumbnail size.

When do thumbnails get generated?

It can take some time to generate thumbnails, particularly for very large images. You can choose when to generate thumbnails:

• On demand : the default is to generate thumbnails when you look at the corresponding record. This means that the first time you open a record there will be a slight delay as the thumbnail is generated, but thumbnails get cached, so the next time you view the record the thumbnail will appear faster.
• On Import : if you select the 'generate thumbnails' option when you import a folder, it will generate thumbnails for all images as you import. The import will take longer, but browsing will be faster.
• On Save : You can choose to 'save with thumbnails' from the File : Save As option. If you do this, then the catalog file will include all the thumbnails.
• On publish : if you include thumbnails in the published website, then the thumbnails will be generated as you publish.

Where do thumbnails get stored? Can I save a catalog with thumbnails?

A copy of thumbnails is stored in the ".axiope" subfolder of your home directory. If you opt to save a catalog with thumbnails, then a copy of all thumbnails will be included in the catalog file. This is useful for sending catalog files to other people, but makes saving / loading catalogs slower.

The "save as" dialog includes an extra button - "Catalog Save Options". Here you have the option to save thumbnails with the catalog. When enabled, thumbnails of all image resources (which are readable by Catalyzer and its plugins) are pre-generated and stored with the catalog. This allows a thumbnail of an image resource to be visible in Catalyzer even when the original image resource is no longer accessible. This can be used, for example, to create catalogs of data stored on CDs. Even when the CD is not loaded in the drive, the thumbnails of its contents are visible in Catalyzer.

It is possible to import an existing catalog at any point of a catalog tree - indeed this ability to combine multiple catalogs is one of the most powerful features of Catalyzer.

You can import a catalog using the Import : File... main menu option, and selecting a catalog file. The imported catalog contents will be inserted into your catalog. You can also use the right-click menu (ctrl-click on Mac); select a folder in the catalog tree, and choose Import : File....

When you first import another catalog, it imports it as a link - so edits to the imported catalog will be reflected the next time you refresh (right-click>Refresh on the root record). You can also Fix a copy of the catalog (right-click>Fix on the root record). This makes a fresh copy of the imported catalog.

A Catalog made by combining three catalogs. Note that these have been imported by reference, so the record names appear in italics to indicate that the records are not editable.

To import a catalog into Catalyzer, right-click on the point in the tree at which you want it imported and select Import>File. Browse to the catalog location (catalogs have an extension of .axz or .axc) The catalog will be loaded into the folder you initially selected.

You can import just the classes from another catalog - this is useful if you set up some useful classes (such as "Protocol", "Publication") and want to use them in many different catalogs. There is a related feature, Template Catalogs, described in the Advanced Features section.

To import the classes from another catalog, select File > Import > Classes and Types. The following screen is displayed: Classes and Types Import Choose the catalog from which to import the class definitions Enter the location of a catalog or click Browse to locate it. You can choose either a catalog (with extension .axz), or a stand-alone type catalog (extension .axt) Click Open. The classes from the given catalog are now in Catalyzer. You can now add records for the imported classes.

One application for importing type catalogs is to control who changes the standard classes and to encourage everyone to structure their data in the same way. One person could be responsible for setting up the classes, ane everyone else could import this central type catalog and enter their own records.

Exporting a catalog

You can export a subset of the catalog as another catalog:

• From the catalog tree (select a folder, choose Export : Catalog from the right-click / ctrl-click menu)
• From the browse or search results window (after you've done a subselection right-click (ctrl-click on Mac) and pick the Export option

Printing is available in various locations within Catalyzer Main menu. You can use File>Print... to print the entire catalog, or the context-sensitive menus (right-click) in the record tree panel and the form list panel to print subtrees (Print). The context sensitive menu in the search panel can be used to print search results.

On selection of print from any of these locations, the Print Options dialog is displayed. This shows the target printer, and data selection options. To change the target printer, or to modify page setup options, click Setup.

The data selection options available depend on the type of data selected for printing. When printing records, the following options are displayed:

• Print current selection or Print entire catalog.
• Include classes - if selected, the class definitions of records in the print output are also printed.
• If Print current selection is chosen, the following options are available to filter the record selection.
• Include subrecords - prints all subrecords of the selected records (but not records referenced by the selected records. This is recursive, printing the root record of a catalog and selecting include subrecords will print the entire catalog.
• Include linked records - will print all records referenced by the selected records.

If Print entire catalog is selected, the above options are irrelevant and not displayed.

When printing classes, the following options are displayed:

• Print current selection or Print entire catalog.
• The remaining options above are not relevant for class printing.
• When ready to print, click Print.

The output will consist of a summary of printed records and classes, followed by the records and classes selected for printing.

Printing requires that you have at least one printer defined with the operating system. If not then an error message will appear if you try to print.

To export a catalog as a .pdf document for viewing or printing, select Export>File... from the catalog tree context sensitive menu, or File>Export>File... from the main menu. A file save dialog will appear. Enter the export file filename, ensuring that the extension is "pdf". Note that if the extension is not recognised, Catalyzer will display an error message.

After a filename has been selected, the same print options as for normal printing of records appears (see the Printing documentation above). However in place of the printer name, you see the selected export filename, and clicking Setup shows a PDF page setup dialog. After selection of options, click Export to produce the PDF.

Catalyzer can turn the data stored in a catalog into a browsable set of web pages, including embedded images for external resources. You can produce your website in a local directory or upload it to a remote web server so that it can be accessed on the Internet.

Generating web pages with Catalyzer is remarkably easy: Select Publish>Publish Catalog from the main menu and then press the Publish button.

The published website for the Mountains example

You can configure how the data is organized on your website, as well as customizing the pages to suit your organization's preferred presentation style. You can also control whether to upload a copy of data files ("resources") with the catalog.

This section describes how to publish your data as a website using Catalyzer.

Any catalog can be published as a website - just use the Publish menu.

Publish Catalog Menu

Select Publish>Publish Catalog from the main menu.

Publish Dialog

Press the Publish button. The following dialog is displayed:

Publish Progress

A summary of your publishing profile is displayed at the top of the window. The current progress of the publishing operation will be displayed. Click Cancel at any time to cancel the operation.

To open the published website in your web browser, click the View button. Currently this only works with websites which have been published to a local directory - for other websites, type in the URL of your site into your browser. You can also set this URL using the publish options page.

The view button shows the website in a browser

To return to the "Configure Publishing" window and change your publishing options, click on the Configure button.

You can also view catalogs using Catalyzer Web Server. This adds Search and Browse functions as well as the ability to combine multiple catalogs. See the Quick Start section (chapter 1) for how to start the Web Server.

Use the Configure Publishing window to control how your data will be published on a website. You can control whether and where the data will be uploaded (local directory, or FTP server), whether to keep certain fields private, and the look and feel of the website.

Configure Publishing

Select Publish > Configure Publishing... from the main Catalog window. The following screen is displayed:

Configure Publishing - Summary

The summary of the publishing options is displayed. This explains where the website will be generated (by default on a local directory, but you can also have Catalyzer upload to a FTP server. The section on Configuring Publishing below has more details.

Publishing your Catalog

After you configure the options in the Configure Publishing window, you can publish you catalog by clicking the Publish button.

Publishing profiles

You can save your customisation of the website as a "profile". This lets you reuse the same settings with multiple catalogs.

Saving a Profile

The Profile field lets you save and delete publishing profiles. A publishing profile is a set of options for your website. Once you have configured the options, enter a name in the Profile field and click Add Profile.

Deleting a Profile

To delete a profile, select it from the drop-down and click Remove Profile. A window is displayed, asking you if you are sure you want to delete this profile. Click OK to confirm.

The default options will generate a website on your local machine. But if you want to upload the catalog and resources to a remote web server, or to change the default colours or title, you can use the publish options outlined below.

Setting the Destination - a local folder, or remote FTP / SFTP server

The Destination page lets you upload the web pages to a local directory or to a remote web server for wider access. This means your catalog will be accessible on the Internet.

It is possible to add password protection to protect uploaded websites - but the precise mechanism depends on your webserver. Ask your system administrator how to add access control mechanisms (the most common method is with .htaccess files for Apache webservers) to make private areas of your website.

Click the Destination page to display the following panel: Destination Page Select an option from the Publish to drop-down list: Local directory FTP server Secure FTP server Enter values in the fields for the deployment method you have chosen. If you are publishing to an FTP or Secure FTP server, enter the name of the computer you are publishing to, and your username and password. If you want your password to be saved with the catalog, check the Save password to catalog checkbox. The password will stored with your catalog, in encrypted form. If you leave this box unchecked, your password will not be stored and you will need to enter it each time you publish your website. You can click the Purge remote directory before uploading checkbox if you want Catalyzer to empty the destination directory before it uploads the newest information for the website. This avoids the directory filling up with unused web files.

Controlling what happens to your data files - the Resources options

The Resources options lets you choose whether the resources (data files) your catalog refers to will be uploaded along with your catalog.

Click the Resources page to display the following panel:

Resources Options

The following fields are available:

Controlling the information which is uploaded : the Catalog optons

The Classes tab page lets you choose the precise information that you want to publish.

Click the Classes tab to display the following panel: The Catalog options let you exclude private fields Select the class of the records that you want to organize. The types belonging to that class are displayed. The following buttons are available in the Catalog options panel: Include Field, Exclude Field Use these buttons to select which fields you want to include in your website. For example, if you select a field and then click Include Field, the field appears in the Included fields panel and will be included on your website. You can also double-click a field to move it from one panel to another. Include All Fields Use this button to publish all fields Exclude All Fields Use this button to publish no fields Move Item Up, Move Item Down Use these buttons to change the order of the fields as they will appear on the website. Sort Fields Use these buttons to sort the fields alphabetically or put the fields back into their original order. You can use the Sort by drop-down list to change the display order for records in list views. You can click Publish to create your web pages, but you may want to configure the options on the other tab pages first.

If the class you select contains List fields, an information icon is displayed next to the Sort by drop-down; hover over the `i' to display the information. You can't sort by a field that is a List type, but if the class contains other types, you can sort by one of them.

Controlling the look and title of the website : the Website panel

The Website panel lets you set the title of the website, and alter the colours.

Click the Website option to display the following screen:

Website look and feel options

The following fields are available:

The Notify options - adding your catalog to a server

The Notify options let you signal a server of your catalog's existence when you publish it.

Notify a server of the uploaded catalog

Catalyzer is intended to be as simple to use as spreadsheets. But it also includes a number of features which make it suitable for integration with complex database applications.

One of the powerful features of Catalyzer is to make catalogs of files. You can import a file or folder, and make a catalog which refers to your data files. Note that links to external data files are referred to as "Resources" in Catalyzer, as resources can link to data on the web (with a http:// location or URL) as well as to local files.

But what happens if you move your files? The catalog will still be pointing at the old location of your data.

Catalyzer includes a powerful feature to reconnect the links to the new location of the files.

Relocating missing resources

Opening the Resources dialog to relocate lost resources

Often you'll have moved all your data files from hard disk to network drive, or onto CD, so you'll want to map resources which were on "C:/My Documents/data" to "H:data/". The resources dialog(Edit : Resources from the main menu) makes this simple. It displays a list of all external files ("Resources") referred to by the catalog. This displays an icon in Green or Red depending on whether the resource can be found.

To fix up a set of resources to the new location (e.g. you moved them from the C:/data drive to the H:/mydata/ drive), just double click on the path and type the new value.

Click Browse to find the new location of missing resources (shown in red)

Searching for missing resources

The dialog above is useful if you've moved all of your data from one directory to another in one go. But what if you've been doing major restructuring of your file organisation, e.g. moving them from a directories like papers/paper1.pdf to papers/2003/nature/naturepaper1.pdf. What happens to your links to data files?

You could map each file individually using the dialog above. But Catalyzer now includes an extremely powerful feature which will reattach the catalog links to your data files even if you move them - and also even if you rename them!

Click the Edit : Find Missing Resources option from the main menu. If there are any missing resuorces in the catalog, this lets you choose the list of top level directories to start the search.

Opening the Find Resources dialog to search for lost resources

Find Resources will search through a set of directories looking for the resources

The way this works is that when you add a link to a file, Catalyzer computes a unique identifier based on the file contents, and stores this with the link. This enables Catalyzer to scan a directory looking for the data files, and reconnect any broken links.

Formula fields can be used to calculate the value of a field from values of other fields in the record. This could be used, for example, to create a field for the full name of a person by concatenating the "first name" and "last name" fields. It can also be used to compose a complicated URL out of separate items in the record.

To access this feature, you have to be in Class Window mode. Add a new field, and click the Formula icon in the field details toolbar (right hand side of the window). An extra entry appears for the Formula:. Here you can type in an expression referring to other fields of the class. For example, %first name% : %last name%, would cause the new field to be populated with the concatenation of the first and last name fields.

You can use any of the following constructions to refer to a field named Xyz:
$Xyz
${Xyz}
%Xyz%
The form with curly brackets is required if the field name contains spaces.

Formulae are evaluated by substitution, so for example, if the value of Xyz was 9, then %Xyz%%Xyz% would evaluate to 99.

You can specify conditional substitutions as follows:
%Xyz?value-1:value-2%
This evaluates to "value-1" if Xyz is not null, and to "value-2" if it is null. If you wish to use a colon inside a formula as part of the result then it should be preceded by a backslash.

You can use Formula Fields to generate links to databases from values in fields. Create two fields, called pubmedid and pubmedurl. Set the field type of the pubmedurl field to Resource, and click the Formula button on the taskbar. Type a formula such as http://www.database.edu/query?id=%pubmedid%. Every record using this class will have a URL assembled from the value in the pubmedid field. For example, if the value of pubmedid was 123 the query would be http://www.database.edu/query?id=123.

Creating a Publication class - changing the pubmed link field to a formula

A formula to construct a link into the Pubmed database

The pubmed link field will be a Resource (URL) composed from the id field. This Formula constructs the Pubmed URL.

Pubmed ID being used to generate a URL via a formula field

You can now enter values for the id field and the link to Pubmed is constructed automatically. Clicking on the Preview icon opens a web browser on the appropriate Pubmed page.

Required fields are an advanced option to assist in data collection or survey completion. They provide a visual indication of data entry remaining to be done. You can tag particular fields as being "required", so that when others come to fill in a form, they can see whether they've added all required information.

To enable the use of required fields, first open the Preferences dialog (Tools>Preferences...) on the main menu). In the Advanced section, select Enable required fields, and click OK.

Now when you edit a field in class editing mode, there should be an extra menu item Set required. Setting this option for a field will add a red icon next to the field name: which changes color to (green) when a value is entered. The icon for all records of that class will also show an incomplete indicator if a required field is not filled in. This changes back to once all values have been entered. To assist in locating the incomplete entries within a catalog, incomplete records cause indicators to appear all the way up the record tree to the catalog root which is only restored to when all required fields in the catalog have been filled in.

Required fields are a useful feature if you want to provide a catalog for other people to fill in - and make sure that they fill in all necessary information.

Changing the class of a record

To change the class of a record, select the record in tree view and select a class from the drop-down list at the top right of the Class/Record panel. A warning window will displayed indicating that when you change the class of a record you lose the values of any fields for which there are no equivalent in the new class.

If you change the class of a record, you may lose some data. This is because the new class may not contain the same fields as the old one. For example, if you change from a "Photo" class which has fields (url, exposure, size) to an "Image" class which has fields (url, size, date), the values for the exposure entries in the original record will be lost. Click OK to confirm the change.

Changing the class of multiple records at a time

In the Browse window, you can change the class of multiple records at a time using the Class selector at the top right of the window. This can be useful for migrating records to a new class.

Migrating all records of a class to another class

In the Class window, select a class, right-click (or ctrl-click) on its name and pick Migrate Class. This moves all instances of a class to a new class.

Extending the class of a record to let it take subrecords

When you start with a blank catalog, the only type of record to which you can add subrecords is the Folder. But you can also make any of your own classes behave like folders - all you need to do is add a field which is a "List of Records". The steps to do this are as follows:

Change to Class view (Class icon on the toolbar, or View > Class on the main menu). Click the Add Field button in the Class/Record panel (the center panel of the screen). The field will be called something like "Field 2". Rename it to something sensible (perhaps "sublist"), in the Field Name: box in the rightmost panel of the window. In the Field type: entry, choose List. In the Elements: entry, choose Record. This makes the field into a list of records - you could also make lists of other types of thing (like Dates, references etc). You should see the icon to this record in the tree pane on the leftmost panel is now a folder icon. (optional) For the Class: entry, you can choose to restrict the contents of the list to a single class. For example, if you had a "Sample" class, you could make a list which could only contain Samples. Switch back to Catalog view. To add a record to the list, right-click in the new list field (in the Class/Record panel) and select Add or Add using Class if you want to specify a class.

You can create your own field types, known as user defined types, by saving a field type and re-naming it. You can also edit the field options for the user defined type. This is particularly useful for complex menus - you could create a complex menu type listing all countries, and reuse this wherever you have a class which uses a Country field.

Creating user defined types

In the Class Window, select a field on which you want to base your own user defined type. In the Field Options panel, click the Save User Defined Type button. Save User Defined Type Enter a name for your user defined type (the name "Country" is used in the builtin mountains example catalog) and click OK. The user defined type is now added to the Field type menu. The new type has the same field options as the field you originally selected. You can re-define the options by editing the user defined type.

Using user defined types

When you add a field, the user defined types appear in the Field Type: menu, beneath all the standard types (Text Box, Menu etc). To use a user-defined type, just set the field type to the newly defined type ("Country" in the above example).

Editing user defined types

The User Defined Types dialog is accessible from the Edit menu. Edit User Defined Types Menu Option Select Edit > User Defined Types. The following screen is displayed: Edit User Defined Types Select the user defined type that you want to edit by clicking it. The field options are displayed in the right hand panel. Edit the field options and close the window. Your changes are applied to the user defined type. You can create user defined types by converting existing field specifications or by adding new types with the type editing dialog. Adding User Defined Types

To edit a user defined type, you can also select a field that uses the user defined type and click the Edit User Defined Type button in the Field Options panel. This button only becomes active if you select a field that uses a user defined type. Edit User Defined Type

You can Add, Remove and Duplicate user defined types, using the toolbar buttons. These options are also available from the right-click menu. To rename a user defined type, double-click on the name in the list.

When you add a field, the user defined types appear in the Field Type: menu of the field details panel.

The use of template catalogs is an advanced option for the creation of catalogs that do not allow class editing. Using this feature you can create a catalog for distribution to other parties so that new records can be added but where they must use the classes exactly as supplied. This can be useful when collecting data from multiple sources. By making the class definitions non-editable, you can ensure that the resulting catalogs can be easily integrated.

To create template catalogs, open the Preferences dialog (Tools>Preferences... on the main menu) then select "Enable controlled editing" in the "Advanced" section, and click "OK".

There should now be an extra menu item on the main "File" menu, "Save as Template...". Any catalog saved using this menu item will no longer allow class editing. Note that this option does not save the current catalog, but creates a new copy, so remember to save in a different location from the current "master" catalog.

Opening this new template catalog will disable any class editing features of Catalyzer. In this mode, you can still create, remove and modify records.

Template catalogs are very useful to help with curation and submission of data - you can create a template catalog containing all the fields which should be filled in, give this to your users, and you can be sure that the filled-in catalogs they return will conform to your format. This is a more powerful alternative to giving out skeleton spreadsheets or documents to data submitters.

You can also use the Required fields feature to ensure that the all the required information is entered into the template catalog.

A number of plugins are available which provide specialised import from particular file types. These do things like extract settings and other header information from data files (for example, the LSM importer extracts images and microscope settings from Zeiss microscope images). One application of the importers is to automatically catalog all the data in CDs or hard disk - Catalyzer plus Plugins will construct a database containing all metadata with links to the data files, so you can search for all images which used a particular laser setting.

Visit www.axiope.com for the full list of available plugins.

The plugins dialog is available from the main Tools menu

The plugins dialog can be accessed from the Tools>Plugins menu. It displays a list of the plugins that are installed, their version and vendor as well as an indication of their licensing. If plugins are installed that are not yet licensed then licenses can be generated in the license manager.

The plugins dialog

Left clicking on a plugin in the list will display more detailed information about the plugin in the panel beneath the main table.

To install a new plugin, click "Install Plugin". This will create a file chooser which can be used to browse to the jar file containing the plugin. After the jar is selected a dialog will appear detailing information about the plugin to be installed. Confirming this dialog will install the plugin. Plugins can also be installed by copying the jar files to the plugins folder in the Axiope home folder (.axiope/plugins in your home directory) and restarting Catalyzer.

To download more plugins from www.axiope.com, click on "Get More Plugins".

Image Importers

The image import plugins read in metadata and image data from a variety of files. The images can be generated at a variety of different sizes. In addition if more than one image is contained in the image file then the user can generate a tiled image where the thumbnail will contain a square of images, either 2, 3 or 4 images wide.

The Biorad Importer imports .pic files from a Biorad MRC 600 confocal microscope. It extracts all the metadata from the file and thumbnails its image stack. The options for the importer allow you to choose the size of the thumbnail and the number of images from which image tiles will be built.

The Zeiss LSM Importer imports .lsm (Laser Scanning Microscope) files from a confocal microscope. It extracts all the selected metadata from the file and thumbnails its image stack. The options for the importer allow the user to choose the size of thumbnail and the amount of images to build an image tile from as well as offering a choice about the detail level of the imported metadata.

The Leica Importer imports .lei files from Leica. These files index a set of tif files containing the image data. It extracts all the metadata from the lei file and thumbnails the tif files. There are no options for image tiling as the lei file contains data about a series of images. One image is created in the image tile per series. If a series contains an image stack, the central image from that stack is extracted as the series image. The normal options for image sizing are available.

The IPLab importer imports .ipl files from IPLab. It extracts all the metadata from the file and thumbnails its image stack. The options for the importer allow you to choose the size of thumbnail and the amount of images to build an image tile from.

The Metamorph Importer imports .stk files from Metamorph. It extracts all the metadata from the file and thumbnails its image stack. Metamorph files are extensions of TIFF and the TIFF plane data is also extracted.The options for the importer allow you to choose the size of thumbnail and the amount of images to build an image tile from.

The TIFF Importer imports tiff files. It extracts the per-plane metadata from the tiff files and thumbnails its image stack. The options for the importer allow you to choose the size of thumbnail and the number of images to build an image tile from.

XML is a standard file format for exchanging structured information. It is related to HTML, the standard for webpages, and many applications including Microsoft Office are now including XML import and export.

Catalyzer uses XML as its file format, so it is simple to use the data entered in a catalog in custom applications.

The native file format of Catalyzer catalogs is .axz. This is the same as the .zip archive format, and contains two XML files: mycat.axc and mycat.axt. The .axc file contains all the records, the .axt file contains the type catalog (all the class definitions).

You can save a catalog as two separate XML files rather than in .axz format - when prompted for the filename (File>Save as), add the extension .axc (as in "mycat.axc"). This will save two XML files ("mycat.axc" and "mycat.axt" in this case).

One use of Catalyzer is as a database submission / curation tool. You can use Catalyzer to prepare and edit well structured information in a form where it can be submitted to a large database repository. Because Catalogs are easy to customise, and they are saved as XML, the integration is simple to code.

One simple way to import data from a database into Catalyzer is to save the data from the tables in "CSV" format, and use the "Import Files" option. You can also go via a spreadsheet, and manually copy and paste the tables into Catalyzer. But if you do this, then you'll need to patch up the links and references between tables yourself (e.g. by changing the field types from "Text" to "Reference"), and also convert the field data types to Date and Number as appropriate.

The Database Import Module built into Catalyzer allows a more sophisticated import of a database, preserving the types and links between tables. However, as with most things to do with databases it requires you to set up a number of parameters for the connection, so is only really suitable for database administrators to run.

The ability to import from databases is available for Catalyzer as an additional plugin. Once installed, the plugin can be accessed either from the main menu (File>Import>Other...) or from the context sensitive menu in the catalog record tree (Import>Other...). Select SQL Database as the data source, then click on Profile properties. A range of configuration options are available.

The connection to the database - "Java DataBase Connector" or JDBC

The database import module uses the standard "JDBC" connection to talk to the database (JDBC is the Java version of "ODBC" on Windows). The JDBC parameters are required to connect to the data source. Please refer to your database vendor documentation on obtaining a JDBC connection to the database. You can specify:

• JDBC Driver
• JDBC URL
• JDBC Username
• JDBC Password

The Data storage options allow you to specify what types of data will be retrieved from the database. The options are as follows:

• Store data - store the data contained in the source database tables
• Store structure - create metadata records describing the structure of the source database tables.
• Store JDBC Parameters - create records storing the JDBC parameters used to extract the data.
• Foreign key map file - some DBMS (notably MS Access) do not allow the export of foreign key relations. The user can specify a file in which they have created these mappings in XML. The importer will use this file in lieu of attempting to retrieve the mapping data from the database.

Once the properties have been entered, click 'Import'. The database should be accessed and retrieved data added to the catalog.

Note on JDBC Drivers - Catalyzer (and the database import plugin) does not include any third party JDBC drivers. Some databases are accessible without any additional drivers (ODBC databases). Others require a driver to be made available to Catalyzer. To do this: first obtain a JDBC driver from the database vendor. This will usually be available as a jar file. You should add the driver to the installed java extensions by copying the jar file to $JAVA_HOME/lib/ext. See
http://java.sun.com/j2se/1.4.2/docs/guide/extensions/spec.html#installed
for more details on installed extensions.

This chapter includes details on all the types of field which you can add to your classes. The information for each field type is presented as follows:

Text field example

Adding a Text field

Text box example

Adding a Textbox field

Menu example

Creating a new menu field

Before the Add button will appear you have to select the node to add the item to - Menus can be nested so Catalyzer needs to know whether to add the item at the top level of the menu, or as a subitem.

You can also copy and paste items from and into the Menu list. For example, when you have a large number of items in a list in Word and you want to add them to a Menu field, you can copy and paste by right-clicking and selecting Copy or Paste.

Example checkbox field

Adding a checkbox field

Example choice field

Adding a choice field

You can also copy and paste items from and into the Choice list. For example, when you have a large number of items in a list in Word and you want to add them to a Choice field, you can copy and paste by right-clicking and selecting Copy or Paste.

All fields can have an optional color set - this differs from a field of type Color; you use the Color field option in a class and you use the Color field type in a record.

Example date field

Adding a date field

Example list field

Example list field, in table mode

Adding a list field

One extremely powerful use of the List type is to create lists of records. To do this, set the Element to be Record. By default this will let you add any kind of record in the list - but you can restrict this to a single class by specifying the Element class.

Example number field

Adding a number field

Example radio button field

Adding a radio button field

You can also copy and paste items from and into the Radio Button list. For example, when you have a large number of items in a list in Word and you want to add them to a Radio Button field, you can copy and paste by right-clicking and selecting Copy or Paste.

Example record field

Example record field expanded inline

Adding a record field

Example reference field

Example reference field, expanded in place

Adding a reference field

Purpose	Use this field to make a reference to a record that is stored in another part of the catalog.
Example	To refer to contact details, for example the person who took a particular photograph.
Edit	Click the Browse button in the field. You can then select a record from the catalog hierarchy and the filepath to that record appears in the Reference field. You can double-click on the Jump button to go to the referenced record, or you can use the "+" icon to expand the contents in line.
Field options
Class	Use this drop-down menu to select a class for the reference if you want to specify that a reference should be of a certain class. The Class menu contains a list of all available classes in the current catalog.

The difference between the Record and Reference field types is that the Record field holds an actual record that you can open and view or enter information for. The Reference field only holds a link to another record; it does not hold an embedded sub-record. You use the Reference field type if many records should refer to the same thing (for example, many Experiments may use the same Protocol, so it would make sense to add a "protocol" field to the Experiment class, and make its type a "Reference to Protocol").

Example resource, with thumbnailing switched on

Adding a resource field

Purpose	Use this field to enter a path to an external resource - a file or URL.
Example	A path to a file location or a URL; this external resource is often what the rest of the information in the record is about.
Edit	Enter the path or URL manually or use the Browse button to select a file. The Preview button opens up the file using the appropriate application - for example if you have a link to a Word document (.doc), it will open up the file in Word.
Field options
File types	Use this list to specify which type of resource is allowed in the field. The default is to allow everything (All Types), but you can select one or more file types to restrict the choice to certain types.
Thumbnail	Click this option to let Catalyzer try and produce a thumbnail image of the resource. Note: it may take Catalyzer some time to access resources that are not held locally .

The Preview button opens the resource using the appropriate application for the file type - so you can use it to pop up Powerpoint for .ppt files, Excel for .xls files, and your image viewer/editor for images.

Use right-click>Import>Folder to generate a catalog of resources from data you have in the file system.

The preferences dialog lets you customise the features of Catalyzer. These include the default folders to store catalogs, file types, importer options, export options, web server options, Catalyzer look and feel, use of system clipboard, miscellaneous advanced options.

The preferences dialog is available from the Tools menu

The general preferences let you set the default folders for saving catalogs.

Setting the default catalog and folders

The file type preferences option lets you choose which importer should be run on which file type. The Import selector at the bottom lets you pick from the importers you have installed.

Choosing which importer to run on which type of file

The Importers panel lets you set the options for each importer you have installed. See the Plugins section for details on installing more importers.

Setting the options for each importer

The Exporters panel lets you set preferences for the exporters which are installed.

Setting the options for exporters

The web server options let you customise the title of the web server built into Catalyzer. You can also change the port number (the default is 5151).

Setting the web server options

You can change the look and feel of Catalyzer using the Appearance panel. On Mac, choosing the "System" look and feel will give Catalyzer the standard "Aqua" look.

Setting the appearance

The clipboard options let you customise the behaviour when you copy and paste tables from a spreadsheet into Catalyzer. The default behaviour is to assume that the first line contains the column headings; unchecking the "File names in first line" options treats the first line as data instead.

Setting the options for exporters

The main advanced options let you configure a number of settings. Two useful ones are Enable controlled editing and Enable required fields which switch on more advanced features. The image cache options let you control how much disk space is used for the thumbnails.

This chapter introduces some ways in which Catalyzer can be used - integrating it with your existing workflows.

Most people just use filenames - and it's very easy to lose track what was in a file like "result123.dat" later on.

With Catalyzer, you can add as much structured annotation as you like to data files - so that when you return to the data, it will mean something to you. You can also capture cross references between data and analysis files, links to publications and presentations.

Some people create a new catalog for each project / experiment they work on. The catalogs are small enough to store all catalogs on the hard disk. If you store the actual data files on CDs, you can add a field to the catalog to note which CD the data is stored on. You could choose to create a new catalog for each dataset you have - or hold all your information in a single catalog.

You can publish the catalogs as websites on your own computer for conveniently browsing your data using a web browser.

If you need to record structured information as you work, you can choose to write on paper and type into the computer later.

You could also set up a custom catalog and get the information into the computer at source - and minimise transcription errors. Using the Resource links, you can maintain references to documents in Word, spreadsheets with results, and images and data files.

Once the information is a catalog, you can search and browse it, and combine information from multiple experiments. If you need to share subsets of your data with colleagues, the hard work of annotating it will already have been done, and you can send them a weblink or the catalog itself.

If you need to send information about data to other people, what are your options at present? You could send the data files as attachments in email, but many data files are large, and people don't like filling up inboxes with data. You could create a document in Word and paste in some of the data, but Word doesn't handle links to external files very well.

With Catalyzer you could create a catalog linking all the data files with your own custom annotation, publish it as a website on a secure server, and just email people the link to the website. They will be able to download the data when they choose, and if they have Catalyzer will have access to the powerful browsing and searching capabilities.

Catalyzer can be used as an alternative to a spreadsheet for gathering and manipulating data.

The features which are useful in this context are the Browse / Search views which allow very convenient sorting and searching. Note also that you can import multiple spreadsheets into a single catalog, and search across all of them. The other useful feature of Catalyzer is that you can have hierarchy, references and links to files and images.

Note also that is is very simple to copy data from Catalyzer into a spreadsheet (from the browse or search windows) - and from a spreadsheet back to Catalyzer ("import spreadsheet"), so you can use each tool for the tasks to which is it best suited - the spreadsheet for graphing and calculations, and Catalyzer for searching and browsing complex structured data.

Data is very valuable - but how much effort goes into annotating it?

If your students use Catalyzer, then the data they've cataloged is significantly more valuable to you when they leave than a collection of ad hoc filenames and lab notebooks. Each member of the group is free to maintain their own catalogs of their own work - but because catalogs can be merged, you can keep a view of all the work going on in the group.

You can also run a Catalyzer Workgroup Server, which lets selected people view the catalogs from different people in the group. You can even edit catalogs over the web using a browser.

With the web publishing built in to Catalyzer, if you need a web database with information to be shared among a group, Catalyzer can help. If the information is already in a spreadsheet or database, you can import it into catalyzer and press the Publish button.

This is very useful for sharing information in a group - such as publications, documents, protocols etc. And it's lot quicker than setting up web pages by hand.

Core facilities have particular data management concerns; backup and archiving of the data which their users gather using their equipment. Catalyzer's ability to extract settings, thumbnails and other information from different data formats makes it an ideal component for improving the record keeping in a facility. Some core facilities would like to gather a minimum of information about each experiment done; for this the Required Fields feature of catalyzer is ideal, so you can ensure you gather all the information.

In this context, the users of the facility would create a catalog for each experiment they ran on the facility, with the minimal annotation filled in. These catalogs could be saved on a network server, and the facility could build up an annotated archive of all data generated. By using the Publish facility, it would be possible to browse all the data using standard web browser (perhaps over the internal network not the internet).

Keeping records using Catalyzer would be a step towards Good Laboratory Practice compliance, which is becoming more important for many research institutions.

Curating data to make quality archives is a valuable and difficult task. Typically datasets are submitted to a database team (as attachments to emails, or via web forms), and need to be edited and checked before they are submitted to the curated database.

Catalyzer's flexiblity in setting data entry forms makes it ideal for this purpose. The database curator can set up the structure of the catalog specifying all the required fields, and the people submitting data can use Catalyzer to enter their data. The database curator can also create Template Catalogs, with some fields already filled out, and controls on what can be added / removed.

The catalogs and data can then be submitted to the database team - and the curation process will be simpler as the information will already be in the correct structure. Catalogs are saved as XML, which makes them simple to add to existing database infrastructure. The submission itself can use the upload facilities built into Catalyzer (which will upload catalogs and data to an FTP server).

This chapter outlines the functions and capabilities of the various Catalyzer products.

Catalyzer is available in several configurations: Catalyzer, Catalyzer Biomedical and Catalyzer Lite. The free version is Catalyzer Lite, and you can upgrade to the full version with a license key, available from Axiope.

Catalyzer

Catalyzer is the full featured version of the product for editing catalogs.

• Catalog size limited by memory

Catalyzer Biomedical

Catalyzer biomedical has all the features of Catalyzer, and adds support for a number of scientific file formats. This supports extracting information embedded in the file - including thumbnail images of the data, notes and settings. For example, the LSM importer extracts images from the LSM file format, and also extracts the Notes field with text comments about the file. The electrophysiology PClamp importer plots graphs of the time series data embedded in the PClamp file, and extracts the settings.

• All features of Catalyzer
• Microscopy and imaging: LSM, TIF, Deltavision, Leica, IPlabs, Metamporph
• Flow cytometry: FCS
• Electrophysiology: Axograph, PClamp, Spike II

Catalyzer Lite

Catalyzer Lite is our free trial version of Catalyzer. It includes all the features of Catalyzer, but limits the size of catalogs you can work with to:

• 100 Records
• Classes limited to 10 fields
• Importers can only be run 10 times
• Reads catalogs of any size

Licenses are available from www.axiope.com. A license is a small text file which will be sent to you via email.

When it is first installed, Catalyzer runs in "Lite Mode" which is restricted to small catalogs and classes with no more than ten fields. Installing a license allows it to run in "Full Mode" where no restrictions are placed on catalogs or classes.

Licenses can be obtained directly from www.axiope.com or they may be available through your organization. Licenses are typically delivered in text format via an email message or a web page. Once you have a license, click the Add License button on the License Manager (Tools > Licenses), paste the text into the window and click OK:

The license menu

Your current licenses

Adding a license

Plugin licenses are available independently from the main Catalyzer license. The license installation process for plugins is the same as for the Catalyzer license - just paste the license text into the license window.

This section includes several tips for using Catalyzer.

How do I access this "right-click" menu? (Mac Users) Many menus in Catalyzer are context-sensitive - on Windows / Unix you use the right mouse button to pop up a menu. Mac users with a single button mouse can hold down CTRL and click to show the menu.

HELP! how do I get started? The quick start guide at the beginning of this manual includes some step-by-step suggestions, starting with the example catalogs (Help>Example Catalogs>General>mountains).

I can't see my catalog using the Web Server. In Catalyzer Lite, there is a restriction of 5 catalogs in the Web Server's list - try going to the Web Server Admin page (Home and Admin) and add/remove the catalogs from the list. Or, better still, upgrade to the full version.

After you have opened a catalog for the first time with the file chooser, you can reopen it more easily by selecting it from the File>Reopen menu. This works even after exiting and restarting Catalyzer.

The TAB key can be used to move around the user interface without needing the mouse.

Catalyzer uses context-dependent popup menus extensively to access functions in the user interface. Click on a panel with the right mouse button (or CTRL click) to show any context-dependent menu associated with the panel.

Catalyzer can make thumbnails for you of most common image types and display them next to resources. To have the thumbnails made, check the Thumbnail checkbox on the resources field specification editor.

You can enable editing in the class view so that you can enter data in the same window as you edit the class. To do this, go to Tools>Preferences>General and check the box: "Allow record editing in class window".

There are built-in examples that you can load straight from the Help menu. You can use these to see what the different element types look like and how catalogs are structured.

The on-line documentation is also available on the web and in printable form (PDF) at http://www.axiope.com/

Axiope can develop custom plugins to import information directly from data files. If you have files of a particular format from which you want header information extracted automatically, please contact support@axiope.com.

Catalyzer can handle changes of field type where there is a logical action to take. For example you can turn a string field into a menu field. The menu will automatically be populated with the values that occur for the string field in the catalog.

Anywhere that you use a complex data type often (such as a menu with many options) you can save the type as a "User Defined Type" and reuse it without any duplication. See "Creating Catalogs, Classes and Records" in the manual.

Little blue icons indicate information tooltips. The tooltips are shown when the mouse hovers over the icon. You can also right-click on them to see the tooltip in its own window.

If you get stuck, email support@axiope.com with your questions.

This chapter is aimed at programmers interested in using catalogs from their own programs - the information is less relevant to other catalyzer users.

This appendix includes some techical information on Catalogs, which will be relevant to programmers wishing to integrate Catalyzer with their existing systems.

Note that more detailed developer information and a development kit is available from dev.axiope.com.

Catalyzer saves catalogs natively as compressed XML - the standard file extension is ".axz". The .axz format is actually the same as the .zip format - so you can extract the catalog and type catalog as XML by using standard zip tools such as WinZip.

You can also save catalogs directly as XML files - by adding the .axc extension to the filename when you "Save As..." (for example, type "mycat.axc" as the filename). This writes two XML files for each catalog: mycat.axc contains the catalog, and mycat.axt contains the classes.

Catalog

A Catalog is a file which contains structured information. It can contain information about other files (such as annotation of data files), or it can be self contained (such as a list of samples or protocols). Like a spreadsheet or database, you can store tables of data in a catalog; but a catalog can also have a structure of folders and subfolders. Catalogs are just saved as files, and you can also publish them as websites.

Class

A class is a type of record, and has a name and a list of fields. An example class could be "Image" which specifies the fields "filename", "width" and "height". Another could be "Reference" with fields "author", "link to pdf", "title", "abstract". Every record has a single class, and is a specific instance of that class - so a record of class "Reference" will have the values filled in for the different fields (like "author", "title", "abstract". In Catalyzer you can create your own classes, and some are created automatically for you when you import data from files or a spreadsheet.

CSV

"Comma Separated Value" - a simple "lowest common denominator" standard file format for tabular data, where the values are separated by commas and each entry starts on a new line. Most spreadsheets and databases will be able to import/export data in "CSV" format. Catalyzer can import CSV files (see the section on importing CSV files).

Field

A Class defines a number of Fields (such as "Author", "Title", "Abstract"). A Record fills in the values for the fields (such as "Bob", "Killer Rabbits", "This paper describes a new breed of dangerous rabbits.") Fields also have a Field Type - such as "Text", "Number", "Date".

Field Type

The basic type of Fields is "Text" - just a single line of text. Catalyzer supports a number of other types, including Dates, Numbers, Menus, Lists, Resources, Text Boxes etc. You can set the Field Type in the Class Editing window, see section Setting The Field Type.

Folder

In a catalog, a "Folder" is a built in class of record which can have a list of subrecords. So it is useful for organising your catalogs; you can make "Folder" records and subrecords in the same way as you make folders to organise your data files. Making a "Folder" record in catalyzer does *not* make an actual folder in the file system - just one internal to the catalog.

Header information

Information about a file which is embedded in the file. For example, JPEG images from a digital camera include some header information which holds the camera settings, image size, and the date the picture was taken. Word documents include header information detailing the title and author of a document. Catalyzer will extract the header information from a variety of formats and automatically populate a catalog with all the information (see section Import Files).

Metadata

Information about data. If your "data" is a list of numbers gathered from a piece of equipment, the "metadata" would be things like the date you gathered it, the settings of the machine, details of the sample you were analysing etc etc. Catalogs are concerned mostly with storing metadata, along with links to the actual data files.

Plugin module

A module in Catalyzer that will import extra information from data files and make thumbnails.

Publishing profile

A set of options that you can configure and apply when building a website, such as the colours and style of your website.

Record

A record is the basic unit of information storage in Catalyzer. Every record has a single Class which specifies which fields must be filled in. For example a class "Publication" may specify you need fields including "author", "date", "journal", "title". A record of class "Publication" is a specific instance - and could be composed of values "Bob", "1 Jan", "Nature", "Rabbits gone crazy".

Resource

A "resource" is a link to a data file (on hard disk, CD or a network drive). It can also be used for a link to a website (a URL such as "http://www.axiope.com"). "Resource" is one of the field types available when you make a class, so you can make references to files from records.

Root Record

The first item in a catalog file hierarchy - when you first start Catalyzer it is a folder called "untitled".

Sub-record

A record that is stored in another record. One of the Field Types available is "Record" - this lets you embed a record in another record.

Thumbnail

A miniature display of an image or datafile which provides a preview. Catalyzer will generate thumbnails from a number of image formats, and display them along with the record in the main window.

Tree view

The view of the hierarchy of records in a catalog, with a structure of folders and subfolders which is similar to the Windows Explorer view of a filesyste,

Type catalog

The structure used by a catalog, including all classes and types. A type catalog does not contain any records. It is saved along with the catalog in the ".axz" file.

User defined type

You can define complex menus for fields to represent e.g. a species taxonomy - but what if you want to reuse the same taxonomy in different fields? This is where a user defined type comes in; you can save the field type and give it a name (e.g. "MyTaxonomy"). This is now a user defined type which you can use in other fields. Section User Defined Types has more details.

URL

The abbreviation for Uniform Resource Locator, the global address of documents and other resources on the World Wide Web. For example "http://www.axiope.com", "file://c:/My Documents/test.doc". Resource fields in Catalyzer use URLs, so you can refer to either files or websites.

Value

A piece of data that you enter into a record for a field. For example, the value for field "title" in a record of class "Book" could be "101 Ways To Catch A Rabbit". A typical record will have a number of values for its different fields.

Catalyzer includes a number of software libraries; this chapter acknowledges the ones used.

Axiope acknowledges the use of the following libraries used by Catalyzer:

Version

This guide supports Axiope Catalyzer 1.2.0.

Examples

The examples and screenshots are taken from the example catalogs that are built into Catalyzer (Help >Example Catalogs).

Conventions

Bold text is used to identify interface components, as in the reference to the Help menu in the previous paragraph.

Italic text is used to identify terms that appear in the glossary.

The following icons are used to identify sections of the text:

Information notes describe important features or instructions.

Caution notes alert you to potential loss of data with certain operations.