gsgs
Posts: 104
Joined: Sun Dec 13, 2015 6:48 pm

Re: 4273pi: Bioinformatics education on low cost ARM hardwar

Sun Dec 13, 2015 6:51 pm

who sells an installed sd-card ?

---------------------

how does it compare with "bio-linux"
[or bio-knoppix[discontinued?]]

DanielBarker
Posts: 72
Joined: Tue May 29, 2012 7:53 am

Re: 4273pi: Bioinformatics education on low cost ARM hardwar

Mon Dec 14, 2015 1:47 pm

Dear gsgs,
who sells an installed sd-card ?
I don't know - but if someone does, we'd love to hear.

The 4273pi project has been thinking of setting up an SD initialising service. The plan would be, people could send us blank SD or microSD cards, and we'd initialise them with 4273pi - either free of charge or at a low cost (e.g. to cover postage).

We have no such service yet, but we'd be interested in trying this on a small scale. Please contact me by email before sending any cards - including an estimate of quantitites, time-scale required, and the country where you're based. We'll see if we can help. You can find my email under "contact", here:

http://4273pi.org/
how does it compare with "bio-linux"
EOS BioLinux has more software, but doesn't work on the Pi. Also, 4273pi includes the materials for a course in bioinformatics, "4273pi Bioinformatics for Biologists". Both projects benefit from debian-med, which has ported a range of biomedical software to the Debian package system.
[or bio-knoppix[discontinued?]]
I regret, I don't know this one.

Best regards,

Daniel Barker

gsgs
Posts: 104
Joined: Sun Dec 13, 2015 6:48 pm

Re: 4273pi: Bioinformatics education on low cost ARM hardwar

Tue Dec 15, 2015 8:11 am

thenks, I sent email.


the main idea is to use the raspberry pi as a second (third,fourth,...) computer to perform
time consuming tasks like aligning sequences, searching/processing/changing large sets
of sequence-data, downloading or uploading large data sets and so on.
These tasks presumably often occur in bioinformatics.

You set up the raspberry-bootable SD-card in your normal computer, copy the needed data to
it, assign the tasks in the autoexec.bat, insert the card into the raspberry, boot the raspberry
and let it run overnight or over weeks or whatever is needed. The result is written back to the
card and the LED somehow indicates when the task has finished (or can it shutdown by software ?)
No display,no monitor needed. You can have dozends of raspberries running this way simultaneously
without taking much space and without heating the room too much.
The cards can be copied and reused later for other tasks.

You just need a raspberry and power supply, that's less than $50 per unit.
The batch files to set up the tasks and the programs to run can be sent over the internenet
to other other users who have the same system.
You can also easily exchange the cards by snailmail instead of uploading

One such raspberry can serve as a SD-copying machine - has it been done ?

4273pi
Posts: 1
Joined: Thu Mar 10, 2016 1:34 pm

Re: 4273pi: Bioinformatics education on low cost ARM hardwar

Thu Mar 10, 2016 9:51 pm

For anyone interested in teaching, learning and using computational biology on the Raspberry Pi: we are delighted to announce release 1.4 of 4273π. Please download it at:

http://4273pi.org

This version includes updated materials and operating system. It should run on any model of Raspberry Pi.

4273π is a freely available, customized distribution of Raspbian GNU/Linux for the Raspberry Pi. It includes 4273π Bioinformatics for Biologists, an Open Access bioinformatics course in modular form.

Check out our peer-reviewed publications on http://4273pi.org/publications, covering higher education, secondary education, research and public events!

Thank you,

Heleen Plaisier, Institute of Evolutionary Biology, University of Edinburgh

gsgs
Posts: 104
Joined: Sun Dec 13, 2015 6:48 pm

Re: 4273pi: Bioinformatics education on low cost ARM hardwar

Fri Mar 11, 2016 9:25 am

is there a version for normal computers ?

DanielBarker
Posts: 72
Joined: Tue May 29, 2012 7:53 am

Re: 4273pi: Bioinformatics education on low cost ARM hardwar

Fri Mar 11, 2016 5:25 pm

Dear gsgs,

4273pi is distributed as an SD/microSD card image for the Raspberry Pi. The teaching material is also available separately, as a zipfile (4273pi_course_material.zip). The zipfile could be useful on other systems too.

We consider the Raspberry Pi to have various advantages for bioinformatics education. See our 2013 paper (http://dx.doi.org/10.1186/1471-2105-14-243). But still: we will be interested in convenient routes to some degree of platform independence.

We will be looking into running 4273pi under QEMU. This could be a simple way to use 4273pi on a greater range of computers. If anyone has tried it already, please do get in touch.

Daniel Barker http://www.ed.ac.uk/biology/people/rese ... id=dbarker

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