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Catalyzer is letting the user do it. It's not technically complicated for the user to understand how to implement their data structures in Catalyzer.

Jeff Shilling, National Cancer Institute

Contents

1 Installation and Platform Support
1.1  What is the difference between Catalyzer Desktop and Catalyzer Server?
1.2  What platforms does Catalyzer run on?
1.3  If I have a trial license for Catalyzer, do I need a new installation for the full license?
1.4  On Linux, which version of the JVM do I need to run Catalyzer Server?
2 Applications
2.1  What is Catalyzer for?
2.2  How is Catalyzer different from a relational database?
2.3  How is Catalyzer different from a spreadsheet?
2.4  Does Catalyzer interoperate with other systems?
2.5  Can I use Catalyzer with a barcode scanner?
3 Catalog Editing
3.1  Can I use a combination of field values as the name of a record?
3.2  If I move my files around, will Catlyzer keep track of them?
3.3  Why can't I use some punctuation characters (e.g. "$", "@" etc) in field names?
3.4  Can a catalog include links to other databases?
4 Import and Export
4.1  Can I import data from spreadsheets?
5 Server
5.1  How is publishing to the Catalyzer Server different from publishing web pages?
6 Future Directions
6.1  When will you have support for data format XYZ?

 

Installation and Platform Support

1.1  What is the difference between Catalyzer Desktop and Catalyzer Server?   

Catalyzer Desktop is used for catalog design and editing. Catalyzer Server is used for catalog archiving and sharing data over the web. Catalyzer Server has a variety of features not available in Catalyzer Desktop such as multi-catalog searching, catalog and file versioning, and logins with group-based access control.

1.2  What platforms does Catalyzer run on?   

Catalyzer is supported on Windows XP, Window 2000, Mac OSX 10.4, Redhat Enterprise Linux 4.0 and Debian 3.1. Other Linux versions may be supported - please contact us.

See the System Requirements for more information on operating system, web browser, and hardware requirements.

1.3  If I have the trial version of Catalyzer, do I need a new installation for the full version?   

No, the same installation works for both. When you buy the full version you receive a new license key that unlocks the extra functions. You install the license key on Catalyzer Server from the admin page.

1.4  On Linux which version of the JVM do I need to run Catalyzer Server?   

Catalyzer Server runs using version 1.5 of the Sun's JVM. If you do not have Java 1.5, or if you experience problems with a non-sun JVM, download and install the version 1.5 of the JRE from http://www.javasoft.com. You can configure the search path for Java in the CatalyzerServer-Service or CatalyzerServer script files by uncommenting the INSTALL4J_JAVA_HOME_OVERRIDE environment variable and setting it appropriately, for example:

INSTALL4J_JAVA_HOME_OVERRIDE=/opt/jdk1.5.0_11

 

Applications

2.1  What is Catalyzer for?   

Catalyzer lets you set up and store information in structured records without you having to be a computer or database expert. The advantage of structured records instead of just documents is that they can be processed (indexed, reused, exported, mined, shared,...) much more easily.

Initially, Catalyzer was developed for biological research scientists who need to record and process complex information about experimental procedures and results.

But it is equally useful in many other areas. Cataloging documents, managing a membership list, or keeping an equipment inventory are some other uses.

2.2  How is Catalyzer different from a relational database?   

Catalyzer has different objectives from relational databases: databases handle large volumes of data very efficiently but you need a good understanding of database design to set one up. The focus in Catalyzer is on being intuitive and easy to use. But we make it easy to migrate catalogs into a database if you need to.

Another big difference is that databases should be designed up-front: you should know what is going in and how it is to be structured before you start. Catalyzer, on the other hand, is about evolving the best structures as you add more data. So you can start straight away and not worry that you may need to change the structure later.

2.3  How is Catalyzer different from a spreadsheet?   

The key difference is structure: because you can put what you like where you like in a spreadsheet, there usually isn't enough structure to merge sheets, mine the data or export it on the web. But if you already use spreadsheets very systematically with headings for each column and one table per sheet, then you will find it very easy to import them into Catalyzer.

Catalyzer forces you to be more precise, (eg by giving types to columns - number, date, color, text, menu selection etc), with the result that you can browse and search the data much more efficiently. And you get tree structures more like a file system.

Most spreadsheets also offer other functions like equations and charting that Catalyzer does not provide. But we do provide a convenient export function to take a subset of a catalog out into a spreadsheet if that is what you need.

2.4  Does Catalyzer interoperate with other systems?   

Yes, with the database plugin, catalyzer can extract and view data from any database for which there is a JDBC connector (that is, almost all common databases).

In addition, Catalyzer stores its catalogs as clean well-structured XML so it is straightforward for a software engineer to write interfaces that import catalogs into existing systems. This means that systems developers can save time and money by getting clients to use Catalyzer as a desktop data submission and access tool instead of developing and distributing custom solutions.

2.5  Can I use Catalyzer with a barcode scanner?   

Catalyzer supports a variety of both USB and bluetooth bar code readers and label printers, including those supplied by our channel partner Brady Corp. Please contact us if interested in a particular make or model.

Axiope is considering tighter integration between Catalyzer and various barcode scanning hardware. If you have particlyar reqirements, do let us know.

 

Catalog Editing

3.1  Can I use a combination of field values as the name of a record?   

Yes. You do this in two steps - first add a field to contain the derived name, then set this to be used as the name of the record by selecting "set as name" from the right-click menu.

To create a derived field, add a normal field and then click the little calculator icon. You then get a formula box where you can specify how the field value is computed. It takes a number of formats as explained in the on-line help. If you already had fields "Title", "First Name", "Last Name": then you could use "%Title% %First Name% %Last Name%" to derive the full name.

3.2  If I move my files around, will Catlyzer keep track of them?   

Catalyzer can search for files that have been renamed or moved, and then correct the links to them in a catalog. The user just needs to specify which local or remote computer systems to search. The utility for doing this can be found under the "Edit" menu, item "Find Missing Resources".

3.3  Why can't I use some punctuation characters (e.g. "$", "@" etc) in field names?   

At the moment, there are some restrictions on the characters which are allowed in a field name - you can use a-z, A-Z, spaces, numbers and ".", but most punctuation characters are stripped out, or replaced with spaces.

The technical reason for this is that catalogs are saved as XML, and we use the field names as XML tags which imposes some limitations.

3.4  Can a catalog include links to other databases?   

Yes, this is one very common use of the derived fields. If the record contains fields for the identity of an item within a database then usually the database entry can be accessed at some long URL composed of the web address and query strings. In Catalyzer you can create a derived resource field where a formula specifies how to construct the URL. In the exported site these act as links to the original database entry.

 

Import and Export

4.1  Can I import data from spreadsheets?   

There are two ways to do this but both require the spreadsheet to be organized in regular tables with headings on each column.

You can just cut out a single table and then select "import -> clipboard" from the right-click menu somewhere on the catalog tree. This creates a new class from the column headings and one record per row.

Alternatively you can save the data as Comma Separated Values (CSV) and import this into Catalyzer with the CSV import option.

 

Server

5.1  How is sharing data on Catalyzer Server different from publishing web pages?   

When you publish web pages, a set of static pages is created. You must republish to update these pages. With the Catalyzer Server, each page is only created when the viewer clicks on a link from their browser. That is, the server generates the pages dynamically. This means that they are up to date, and, more importantly, they offer a much wider range of views on the data.

For example, the server lets you search several catalogs and generates new pages for the search results. It also offer logins, group creation, and access control for privately sharing data.

 

Future Directions

6.1  When will you have support for data format XYZ?   

This depends on demand - contact us with specific queries.

For highly specialized data formats that are used only by a small number of people, it is unlikely that support will be included among the standard plugins. In this case we may be able to help by developing plugins specifically for your requirements on a consultancy basis. Just contact us as above.

 

Axiope is a pioneer in the development of cutting edge software solutions for biology and biomedical scientific and clinical research, that integrate bio banking, image management, laboratory specimen tracking, and inventory management, using informatics tools that provide laboratory notebook entry options, powerful search, data management and reporting options.
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