Running JCoast

Before you start using JCoast it is important to understand how and where JCoast is connected to the workflow of microbial (meta)genome analysis and how to use JCoast from a technical point of view (the requirements). This Overview Page will help to become familiar with the JCoast principle.

JCoast is a Next Generation Software Solution which allows you to view, compare and further analyse microbial (meta)genomic data within a precomputed database (the prerequisite).

1. What is a precomputed database of your (meta)genome(s)?

Like you first have to sequence your genetic marker of choice to conduct e.g. a phylogenetic analysis, after sequencing of (meta)genomes you first have to preprocess your genomic data by a bioinformatics pipeline before you can extract any biological meaning from the data. This preprocessing includes the prediction of open-reading-frames and the (automatic) annotation of all the predicted ORFs. The results of the annotation are normally written into a relational database system such as MySQL.

Such preprocessing you can (1) do by your own, (2) use a web-based service, or (3) commission a service company.

2. What kind of precomputed database do you need to use JCoast on top of it?

JCoast relies on the GenDB 2.2 database model which is based on a relational database backend such as MySQL. GenDB is a widely used and freely available genome annotation system for prokaryotic genomes. Actually, JCoast is a GenDB extension which can be independently used as soon as an appropriate database is available.

All you need is a precomputed MySQL database in the GenDB 2.2 format (see 1.). JCoast reads and writes information from/to this database.

3. How can you connect JCoast to such precomputed database?

There are two basic options: You can host the database within a local MySQL installation and directly access it by JCoast or you can access a remote database on a dedicated server via the JCoast Web Service.

This principle is also illustrated by the scheme on the right.

Finally, we have to discuss how to start/use JCoast itself.

Here, you have two options plus a demo solution we offer for beginners. All you need is Java version 6 installed on your local computer (check).

• We recommend to start JCoast always from jcoast.net via the Java Web Start technology (see left block 'Run Latest Version'). This option ensures that you always work with the latest stable JCoast version. Currently, JCoast is updated and extended nearly every month.

• Alternatively, you can download a packed .jar file. It contains all libraries required and can be locally installed. This option gives you also access to older JCoast versions.

If you are new to JCoast most properly you do not have access to a JCoast-ready database so far. In this case, just follow the Quick Live Test instructions to explore a demo database (on our servers) via the JCoast Web Service route.

For more information follow the links below. Have fun using JCoast!