NAVIGATING THROUGH THIS PRESENTATION MATERIAL

• this presentation is made using S5 presentation system
• press page down to move to next slide
• press page up to move to previous slide
• press t to change to toggle from presentation mode to text mode
• visit http://meyerweb.com/eric/tools/s5/ for more information
• S5 uses XHTML( content) Javascripting (dynamic aspects) and CSS (layout)
• Podium is similar presentation system that uses PHP instead of Javascripting

BIO-NIX : A New Distro/Stack for Biotech people

Deepan Chakravarthy N

SpikeSource, Bangalore.

http://users.kaski-net.net/~deepan

codeshepherd AT yahoo DOT com

What is BIO-NIX ?

RPM based distro for Biotechnologists.

Would contain software packages widely used by biotech people.

Will have local database of widely used genome.

Kernel with drivers to interface microscope, cellcounters, sequencers etc.

Yum and Apt preconfigured to use Biotech related package repositories.

Why do we need BIO-NIX ?

Biotech people are illiterate about computers.

Developers are mostly hobby programmers who don't care about cross platform compatibility.

Most packages are tarballs. RPM and DEB support is not there.

Tarball and RPM version mismatch.

Targeted users

Medicine: Research Institutes, Hospitals

Drug Discovery : Cell Simulators, Chemo Informatics.

Clinical Trials: Genome and Protein database, Clinical data mining.

Bioinformatics: Bioperl, Biopython, Biojava, BioPHP.

Biophysics: protein-ligand binding simulations, Protein Structure prediction.

Bioprocess: Reactor Simulation, Reactor operation.

Technical Details

Anaconda - the fedora installer

directory tree of fedora iso

creating yum, apt repository; configuring yum, apt

creating a web interface to access the genome and protein databases.

creating RPM and DEB from tarballs

packing Biotech related screensavers

Anaconda

Anaconda - the fedora installer

written in python

Allows user to select packages for installing

Looks for specific location in the fedora ISO for RPMs

Fedora CD1 Directory Structure

/mnt/cdrom |----> Fedora
|                    |----> RPMS -- binary packages
|                    `----> base -- information on this release of Fedora
|                                       Core used by the installation process
|----> images -- boot and driver disk images
|----> isolinux -- files necessary to boot from CD-ROM
|----> README -- this file
|----> RELEASE-NOTES -- the latest information about this release
|                                       of Fedora Core
`----> RPM-GPG-KEY -- GPG signature for packages from Red Hat