7 Bioinformatics Projects

These are 7 Bioinformatics Projects being developed continuously by developers
to increase working efficiency of Bioinformatics Professionals and computational Biologist.

7 Bioinformatics Projects are:

1. BioJava:

The BioJava Project is dedicated to providing Java tools for processing biological data which includes objects for manipulating sequences, dynamic programming, file parsers, simple statistical routines, etc.

2. BioPerl:

The BioPerl project is an international association of developers of Perl tools for bioinformatics and provides an online resource for modules, scripts and web links for developers of Perl-based software.

3. BioXML:

A part of the BioPerl project, this is a resource to gather XML documentation, DTDs and XML aware tools for biology in one location.

4. Biocorba:

- Interface objects have facilitated interoperability between bioperl and other perl packages such as Ensembl and the Annotation Workbench.
- However, interoperability between bioperl and packages written in other languages requires additional support software.
- CORBA is one such framework for interlanguage support, and the biocorba project is currently implementing a CORBA interface for bioperl.
- With biocorba, objects written within bioperl will be able to communicate with objects written in biopython and biojava (see the next subsection).
- For more information, see the biocorba project website.
- The Bioperl BioCORBA server and client bindings are available in the bioperl-corba-server and bioperl-corba-client bioperl CVS repositories respecitively.

5. Ensembl:

- Ensembl is an ambitious automated-genome-annotation project at EBI.
- Much of Ensembl\'s code is based on bioperl, and Ensembl developers, in turn, have contributed significant pieces of code to bioperl.
- In particular, the bioperl code for automated sequence annotation has been largely contributed by Ensembl developers.
- Describing Ensembl and its capabilities is far beyond the scope of this tutorial The interested reader is referred to the Ensembl website.

6. bioperl-db:

- Bioperl-db is a relatively new project intended to transfer some of Ensembl's capability of integrating bioperl syntax with a standalone Mysql database (http://www.mysql.com/) to the bioperl code-base.
- More details on bioperl-db can be found in the bioperl-db CVS directory at http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-db/?cvsroot=bioperl. It is worth mentioning that most of the bioperl objects mentioned above map directly to tables in the bioperl-db schema.
- Therefore object data such as sequences, their features, and annotations can be easily loaded into the databases, as in $loader->store($newid,$seqobj).
- Similarly one can query the database in a variety of ways and retrieve arrays of Seq objects.
- See biodatabases.pod, Bio::DB::SQL::SeqAdaptor, Bio::DB::SQL::QueryConstraint, and Bio::DB::SQL::BioQuery for examples.

7. Biopython and biojava:

- Biopython and biojava are open source projects with very similar goals to bioperl.
- However their code is implemented in python and java, respectively.
- With the development of interface objects and biocorba, it is possible to write java or python objects which can be accessed by a bioperl script, or to call bioperl objects from java or python code.
- Since biopython and biojava are more recent projects than bioperl, most effort to date has been to port bioperl functionality to biopython and biojava rather than the other way around.
- However, in the future, some bioinformatics tasks may prove to be more effectively implemented in java or python in which case being able to call them from within bioperl will become more important.
- For more information, go to the biojava http://biojava.org/ and biopython http://biopython.org/ websites.

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