[Bio-Linux] Mail2:The question arises from where comes the software and how comes it to Biolinux 7

[Sasa Paporovic]

To2: The question arises from where comes the software and how comes it to Biolinux 7 ?

For this let us see where the source is.

Mostly it begins on Debian Linux. There is a team that call itself Debian-Med:

http://wiki.debian.org/DebianMed

Andreas Tille is one of the most active members.
They decide in the best of there knowledge what bioinformatic software is good for Debian and, properly more remarkable, they do the packaging and system integration job.

S. Möller, H. N. Krabbenhöft, A. Tille, D. Paleino, A. Williams, K. Wolstencroft, C. Goble, R. Holland, D. Belhachemi, C. Plessy (2010) "Community-driven computational biology with Debian Linux" BMC Bioinformatics, 11(Suppl 12):S5 

A. Tille, S. Möller, M. Hanke, Y. Halchenko (2011) "Debian Med - Integrated software environment for all medical purposes based on Debian GNU/Linux", Med at Tel 2011

[Please cite them also if you use the bio-software on Ubuntu]


“And how comes Ubuntu in the game?”

Ubuntu is a bit parasitic to Debian. Oh, let me correct that. It is a symbiont.
They derive the Software for the actual development branch of Ubuntu(just finished Ubuntu13.04 development) from the actual testing branch of Debian(it was from Debian 7 testing).

The other way around Ubuntu provide problem information and bugfixes for the Debian project. Additional many Ubuntu developers are also Debian developers(or the other way around).

To user terms of genealogy:

Debian is the mother and Ubuntu the daughter.

“And what is the relation to Biolinux?”

Tim Boot(grandmaster level) and team(grandmaster level) do the same as the Ubuntu people with Debian. They derive, but not from Debian direct. Instead they derive from Ubuntu long term supported Versions - > Ubuntu LTS(10.04 for Biolinux 6; 12.04 for Biolinux 7) 

With this Debian ist the grandmother, Ubuntu the mother and Biolinux the douther.

Field, D., Tiwari, B., Booth, T., Houten, S., Swan, D., Bertrand, N. and Thurston, M. 2006. Open Software for biologists: from famine to feast. Nature Biotechnology 24, 801 - 803. 

So, to summaries the game:

Sourcecode(bio) --Andreas Tille et al.-->Debian(sooner or later in testing)

--Ubuntu developers--> Ubuntu LTS(all even years;the .04 version)

--Tim Booth et al.-->Biolinux

The reader with attention have recognized that there are only every two(even) years are Ubuntu LTS-Versions(6.06 in 2006, 8.04 in April,10.04 in April 2010, 12.04 in April 2012 and the next will be 14.04 in year 2014 → you see xx.04 means April as release date for final).

That is not good to get only every two years fresh scientific sofware/software versions, which is the consequence of the fact that Biolinux is derived only on the LTS versions and their 2 year release cycle.

Keep cool you will be helped!

Tim(and grandmaster-team) are incorporating additional software in Biolinux and bring new software version on over there own repository:

http://nebc.nerc.ac.uk/bio-linux/ unstable bio-linux

, which is enabled by default in Biolinux.

They give also back to Ubuntu and Debian and prepare with this also the next versions).

Wow, what a job!

Is this now all?

No, there is still a other bridge on which new software could migrate into Biolinux.

Let us have a look.

→ Mail3: What is a backport?



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