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 Forum index » Advanced Topics » Puppy Derivatives
A new born BioPuppy Linux
Moderators: Flash, JohnMurga
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asprakash

Joined: 29 Oct 2007
Posts: 16

PostPosted: Thu 15 May 2008, 02:57    Post_subject:  A new born BioPuppy Linux  

Hello all,
I gladly inform you that, our first beta version of BioPuppy Linux is out now. My motivation in this project is, want to get some contributions from bioinfo people.
I came to know that, almost they are [ I m talking about in India, No idea about in other countries ] using FOSS softwares. But they are using these tools in Windows platform. Coz they are fear about Linux, especially about commands. I am working in Embedded system field. I used this Puppy Linux for one of my embedded linux project. Its an great user friendly Linux compare with others. My idea is, want to provide an dedicated, user friendly Linux OS for them. So that atleast they will try to use the linux first. Later may be they will contribute for FOSS. BioPuppy is a community project for educational and learning purpose for bioinfo people.

Download

BioPuppy main page and download page is here, http://www.biopuppy.org

About BioPuppy

BioPuppy OS is an electronic workbench for bio-informatics and computational biology. It has been designed to meet the needs of beginners. BioPuppy is available as a live CD cum installation CD [and in USB Pen drive] and containing all the required software to boot the computer with ready to use bio-informatics tools. BioPuppy is based of the Puppy Linux. The another objective of this BioPuppy is small in size. Our estimated size of BioPuppy is ~150MB.
BioPuppy derived from Puppy-3.01-seamonkey Linux.

Biology softwares included

Sequence Analysis Tools : Sim-4, Tigr-Glimmer 2, Genewise, Muscle, Sigma,
HMMER, Clustal-W, mafft

Structure Prediction Tools : mfold, gibbs

Protein Structure Analysis Tools : Garlic, Rasmol

Phylogenetic Analysis tools : Fast DNA, Phylip, Phylodraw

Protein Modeling : Modeller,

Docking : MGL Tools ( Autodock tools, Python Molecular Viewer (PMV), Vision)

System Biology : Copasi

On-line tools : BLAST, EMBOSS

Dear all, I read about the license and issues for assigning the name of puppy derivative. But i confused now. "BioPuppy" is ok (or) I want to change it like BioPup.
But i dont like this name, BioPup. One more doubt, I found we have very few .pup packages for Bioinfo. We have prepared .pet packages for all those which we have added. I would like to share this .pet packages with others. Let me know, to whom i want to contact for upload it in http://dotpups.de/dotpups/
Awaiting for for your valuable replies and comments about BioPuppy.

-Regards,
Prakash.A.S

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Lobster
Official Crustacean


Joined: 04 May 2005
Posts: 15117
Location: Paradox Realm

PostPosted: Thu 15 May 2008, 03:38    Post_subject:  

Smile Congratulations.

You can pm (private message) Barry about the name from this forum
but it should be OK. I would add a link to Barrys page on your website.

By creating your programs as sfs or .pets you will be able to easily upgrade to later versions of the Puppy base.

you might like to announce it here
http://puppylinux.org/home/latest-news

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muggins

Joined: 20 Jan 2006
Posts: 6689
Location: lisbon

PostPosted: Thu 15 May 2008, 04:28    Post_subject:  

asprakash,

well done. The only thing you might get queried on though is:

Quote:
will boot from a minimum PC/Laptop with 586Mhz CPU and 32Mb RAM


Puppy will boot with less than 128M RAM but how much can be accomplished depends on which applications are used, & how much resources they require. I've had firefox running with 64M Ram, and a 250M swap partition, and it would slow to a snail's crawl after about an hou'r use. I've no idea on how resource hungry your bio-apps are though?
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asprakash

Joined: 29 Oct 2007
Posts: 16

PostPosted: Thu 15 May 2008, 05:16    Post_subject:  

Thank you Lobster. I have sent an mail to him reg this issue and waiting for his reply.

Dear Muggins, currently we are using P3 500MHZ PC with 128MB RAM. Puppy is working fine. But we have added some graphics supported bioinfo tools, like Copasi, MGL Tools, Rasmol...etc. Every thing is working fine. But only the MGL tool taking more time to start running. I recommend 256MB of RAM for using this tool.

-Regards,
Prakash.A.S
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muggins

Joined: 20 Jan 2006
Posts: 6689
Location: lisbon

PostPosted: Thu 15 May 2008, 05:25    Post_subject:  

Hi Asprakash,

I just meant that you should perhaps update your website to reflect a realistic minimum amount of RAM.
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fzsolt

Joined: 11 Aug 2007
Posts: 21

PostPosted: Thu 15 May 2008, 10:18    Post_subject: is MD5 hash OK?  

Seems to be a very interesting puplet. I am going to show it to my colleagues doing mol. biology.
Is the MD5 hash shown on the homegpage correct? I have downloaded the iso two times. It was 196321280 bytes and I got 349b2adff71d3e7df16520cb488110ad for the MD5 check.
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asprakash

Joined: 29 Oct 2007
Posts: 16

PostPosted: Thu 15 May 2008, 10:44    Post_subject:  

Thank you fzsolt. You are correct. Its my mistake. I checked the MD5, once again. What you got the MD5 is correct... I have updated it in the wiki page.
Thank you for encourage me.. Very Happy

-Regards,
Prakash.A.S
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Aitch


Joined: 04 Apr 2007
Posts: 6825
Location: Chatham, Kent, UK

PostPosted: Sun 18 May 2008, 08:27    Post_subject:  

@asprakash

Hi I've had a look at your Biopuppy & hope it soon goes from beta, as it looks a very useful learning tool

I particularly like the fact you put help files in the menu

I like it so much I'm going to show it off for you!

Windoze converts will feel more at home Very Happy



Good Luck

Aitch
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ttuuxxx


Joined: 05 May 2007
Posts: 10829
Location: Ontario Canada,Sydney Australia

PostPosted: Sun 18 May 2008, 10:00    Post_subject:  

Hi I like the concept of this variant
I was just wondering why you didn't change any Icon or even give icons to your bio menu?
If you would like I could give you a hand with it?
ttuuxxx

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asprakash

Joined: 29 Oct 2007
Posts: 16

PostPosted: Mon 19 May 2008, 06:07    Post_subject:  

Thank you Aitch and ttuuxxx for your encouragement . Smile
Actually, this project intention is, primarily on providing a user friendly Linux for biology. Not yet started to concentrate on themes and others. Really all your contributions are appreciated. You are always welcome... Very Happy

-Prakash
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MU


Joined: 24 Aug 2005
Posts: 13642
Location: Karlsruhe, Germany

PostPosted: Mon 19 May 2008, 06:20    Post_subject:  

Quote:
I found we have very few .pup packages for Bioinfo. We have prepared .pet packages for all those which we have added. I would like to share this .pet packages with others. Let me know, to whom i want to contact for upload it in http://dotpups.de/dotpups/


Great, please see:
http://murga-linux.com/puppy/viewtopic.php?t=28930
Mark

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asprakash

Joined: 29 Oct 2007
Posts: 16

PostPosted: Fri 27 Jun 2008, 01:50    Post_subject: New site launched for Biopuppy Linux  

Hello all,
Thank you for all your supports and special thanks to Mr.Barry Kauler accepting the name "BioPuppy" for this biology derivative.
A new site http://biopuppy.org has launched for biopuppy Linux. As of now, it is compatible with Mozilla, firefox and opera web browsers. But not with IE. You will face some problems when you download iso image from IE web browser. I will rectified this problem, soon. I recommend you to use firefox WB.

-Prakash.
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asprakash

Joined: 29 Oct 2007
Posts: 16

PostPosted: Mon 16 Nov 2009, 03:35    Post_subject: Biopuppy 2.0 beta version released!.  

Tremendous support from all over the world for the first version of Biopuppy, today we released second version BioPuppy Linux. Even we have restricted target audience are only from Bioinformatics, more than 500+ Universities/colleges and thousands of individuals downloaded and using BioPuppy Linux. My sincere thanks to all the community members for providing such a great easy to use Linux and community support for Puppy Linux. I dedicated this second version of BioPuppy 2.0 to all the Puppy Linux contributors and community members.

Whats new in BioPuppy 2.0::
- Updated all the existing bioinfo tools available in the biopuppy 1.0
- Added Adun, Artemis, Gromacs, R, Bioconductor, Biofox and Biobar tools
- Added Bioinfo repository in biopuppy portal. You can download any other Bioinfo tools and install
- Updated latest Linux kernel version on Puppy Linux 4.2.1
- More user's friendly, Desktop widgets and Audio/Video plaugins
- And more. Try today. visit www.biopuppy.org and try Biopuppy 2.0.


-Thanks & Regards,
Prakash a s
Coordinator,
Biopuppy team,
www.biopuppy.org
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infromthepound

Joined: 12 Jun 2009
Posts: 133

PostPosted: Sun 14 Aug 2011, 18:54    Post_subject: Update?  

Hi All,
Is there an updated version of Biopuppy?
The one here is based on 4.2.1, and dated Nov 2009.
Thanks, John
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