The Project Management System and Other

Services at Bioinfomatics.Org

Gary Van DomselaarBioinformatics.org &

Wyeth Research / Genetics Institute

Bioinformatics.Org has supported the advocates of freedom and openness in bioinformatics, primarily by hosting the development of Open Source software and general information projects.

As the popularity of the web site has grown, other services have been added:

•Online Databases

•Online Analysis Tools

•Educational Resources

•Mailing Lists & Forums

Introduction

A large number of services are available to facilitate software

development projects:

Software Development

The core project hosting software is based on the popular SourceForge™

distribution.

–Personal Customizable Account

–Task Manager

–Mail Aliases

–E-mail Lists

–CVS Repository

–File Server / FTP Space

–Bug-Tracking System (Public & Private)

–Discussion Forums (Public & Private)

–SSH Account

The Project Management System: Software Development Services

Software Development: Homepage Hosting

Software Development: Forums

Software Development: Bug Tracking

Software Development: Mailing Lists

Software Development: CVS Code Repository

Software Development:FTP

Software Development: File Release.

Software Development: Project News

Software Development: Personal Page

The Project Management System: The Software

Apache Currently the most popular web server on the Internet

CVS CVS is the Version Control system that we use, for both our developmentand that of the projects.

CVSWeb A script to allow easy viewing of live CVS repositories.

MySQL MySQL is a true multi-user, multi-threaded SQL Relational databaseserver. MySQL is a client/server implementation that consists of a serverdaemon mysqld and many different client programs and libraries.

GNU MailMan Mailman is software to help manage email discussion lists, muchlike Majordomo and Smartmail. Mailman gives each mailing list aweb page, and allows users to subscribe, unsubscribe, etc. over theweb.

The Project Management System: The Software

PHP PHP is a server-side, cross-platform, HTML embedded ,OOP scripting Language with multiple database connectivitysupport. Powerful and easy to use, PHP is a very popularembedded scripting language.

RedhatGNU/Linux

Red Hat GNU/Linux is a powerful, extreme ly stable, UNIX-like computer operating system that provides a highperformance computing environment for both server anddesktop PCs.

OpenSSH OpenSSH is a program that a llows you to open an encryptedconnection to another computer. It allows remote execution ofcommand and copying of files from one machine to another.

Mod_SSL The mod_ssl pro ject provides strong cryptography forthe Apache webserver via the Secure Sockets Layer(SSL v2/v3) and Transport Layer Security (TLS v1)protocols by the he lp of the Open Source SSL/TLStoolkit OpenSSL, whic h is based on SSLeay.

Other Services at Bioinformatics.Org

• Online Databases – Immigrant Genes

– Molecular Linux

• Online Analysis Tools– COMBOSA3D

– SeWeR

– SMS

– Sequence Extractor

• Educational Resources– Bioinformatics FAQ

Home Page

• Mailing Lists & Forums– BiO News Home Page

– BiO Bulletin Board

– Job Announcements

– Bioclusters

• Other Resources– BioBanner

– BioMail

Online Databases: Immigrant Genes

• The Immigrant Genes database contains genes that have immigrated or been transferred from one species to another. Such knowledge is useful for studies that rely on phylogenetic and/or sequence similarity information.

• Currently the database contains genes predicted to have immigrated from Proteobacteria or Cyanobacteria to eukaryotes.

Online Databases: Molecular Linux

Online Databases: Molecular Linux

Online Analysis Tools:Sewer

Online Analysis Tools: Sequence Extractor

Online Analysis Tools: Sequence Manipulation Suite

Online Analysis Tools: COMBOSA

Educational Resources: Bioinformatics FAQ

Mailing Lists & Forums: BiO News

Mailing Lists & Forums: Bioclusters

Mailing Lists & Forums: Job Announcements

Mailing Lists & Forums: Bioinformatics Bulletin Board

Other Resources: BioMail

Other Resources: BioBanner

Future Plans

• Calendaring System

• Polling System

• Documentation Manager

• Distributed Web Services

Future Plans

• XML RPC / SOAP / CORBA / MONO

• PIPER