The Project Management System and Other Services at Bioinfomatics.Org. Gary Van Domselaar Bioinformatics.org & Wyeth Research / Genetics Institute

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Edwin Hodge
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2 The Project Management System and Other Services at Bioinfomatics.Org Gary Van Domselaar Bioinformatics.org & Wyeth Research / Genetics Institute

3 Introduction 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

4 Software Development A large number of services are available to facilitate software development projects: The core project hosting software is based on the popular SourceForge distribution.

5 The Project Management System: Software Development Services Personal Customizable Account Task Manager Mail Aliases Lists CVS Repository File Server / FTP Space Bug-Tracking System (Public & Private) Discussion Forums (Public & Private) SSH Account

6 Software Development: Homepage Hosting

7 Software Development: Forums

8 Software Development: Bug Tracking

9 Software Development: Mailing Lists

10 Software Development: CVS Code Repository

11 Software Development:FTP

12 Software Development: File Release.

13 Software Development: Project News

14 Software Development: Personal Page

15 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 development and 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 database server. MySQL is a client/server implementation that consists of a server daemon mysqld and many different client programs and libraries. GNU MailMan Mailman is software to help manage discussion lists, much like Majordomo and Smartmail. Mailman gives each mailing list a web page, and allows users to subscribe, unsubscribe, etc. over the web.

16 The Project Management System: The Software P HP P HP is a server-side, cross-platform, HTML e mbe dded, OOP scripting Langua ge with multiple database connectivity support. Po werful a nd easy to use, PHP is a very popular e mbedde d scripting la ngua ge. Redhat G NU/Linux Red Hat G NU/Linux is a powerful, e xtre me ly stable, UNIX like co mputer o perating system that provides a high performa nce co mputing e nvironme nt for both server and deskto p PCs. Ope ns S H Ope ns S H is a pro gra m that a llo ws you to ope n a n encry pted connection to a nother co mputer. It allows re mote executio n of comma nd and co pying of files fro m o ne mac hine to a nother. Mo d_ssl The mo d_ssl pro ject provides strong crypto gra phy for the Apache we bserver via the Secure Sockets Layer (SSL v2/v3) and Tra nsport Layer Security (TLS v1) protocols by the he lp of the O pen Source SSL/TLS toolkit O pe nssl, whic h is based o n SSLeay.

17 Other Services at Bioinformatics.Org Online Databases Immigrant Genes Molecular Linux Educational Resources Bioinformatics FAQ Home Page Mailing Lists & Forums Online Analysis Tools COMBOSA3D SeWeR SMS Sequence Extractor BiO News Home Page BiO Bulletin Board Job Announcements Bioclusters Other Resources BioBanner BioMail

18 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.

19 Online Databases: Molecular Linux

20 Online Databases: Molecular Linux

21 Online Analysis Tools:Sewer

22 Online Analysis Tools: Sequence Extractor

23 Online Analysis Tools: Sequence Manipulation Suite

24 Online Analysis Tools: COMBOSA

25 Educational Resources: Bioinformatics FAQ

26 Mailing Lists & Forums: BiO News

27 Mailing Lists & Forums: Bioclusters

28 Mailing Lists & Forums: Job Announcements

29 Mailing Lists & Forums: Bioinformatics Bulletin Board

30 Other Resources: BioMail

31 Other Resources: BioBanner

32 Future Plans Calendaring System Polling System Documentation Manager Distributed Web Services

33 Future Plans XML RPC / SOAP / CORBA / MONO PIPER

Lesson 7 - Website Administration

Lesson 7 - Website Administration If you are hired as a web designer, your client will most likely expect you do more than just create their website. They will expect you to also know how to get their