Most wanted
From Bio.scipy.org
Contents |
If you would like to know how to do something such as How to use Python to do X, post it here. The idea of this page is to create a list of topics, articles, interests that people from the community are interested in so that those who are interested in contributing/writing cookbook, tutorials, programming guides, can get some ideas of what is wanted!
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Cookbooks Wanted
- Module to perform sequence maniplations, ie. reverse complement, DNA->RNA, RNA->protein, etc.
- This is one of my favorite parts of BioPERL. (I used to use PERL, eek!)
- I hate constantly rewriting code to do this
- FASTA Reader
- FASTA Writer may be useful as well
- Controlling other programs with Python using subprocess
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Tutorials Wanted
- Blast output parsing
- Tutorials to go with Writing code that doesn't suck from the programming guide section.
- Parallelizing w/o Threads
- Most bioinformatics problems are easily parallelizable in concept but rarely done in practice.
- Really? I'm under the impression most algorithms in bioinformatics are intractably procedural, though I can see that while sequence alignment is O(mn), multiple pairwise alignments can take place simultaneously on multiple processors. But, to quote Dr. Henry Neeman, that's "embarassingly parallel", while many other problems are not. --Chris Lasher
- Multi-CPU machines are becoming fairly ubiquitous in academic settings and we should write code to take advantage of this.
- Python has limited support to take advantage of multicore systems. More importantly, multicore systems are not magic and inherently wonderful blessings, but are in fact a challenge, because now we have twice (soon to be four times) the cores trying to squeeze data into a tiny little cache, through the same buses to the RAM and hard disk, and into and out of a singular network connection. It is not an easy problem to solve, but here's a brief listing of parallel solutions in Python not based on threads. (That there's no clear winner is yet another issue to consider.) --Chris Lasher
- IPython1
- PyMPI
- mpi4py
- Parallel Python
- Pypar
- Python has limited support to take advantage of multicore systems. More importantly, multicore systems are not magic and inherently wonderful blessings, but are in fact a challenge, because now we have twice (soon to be four times) the cores trying to squeeze data into a tiny little cache, through the same buses to the RAM and hard disk, and into and out of a singular network connection. It is not an easy problem to solve, but here's a brief listing of parallel solutions in Python not based on threads. (That there's no clear winner is yet another issue to consider.) --Chris Lasher
- Most bioinformatics problems are easily parallelizable in concept but rarely done in practice.
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Programming Guides Wanted
- Links to other good articles?
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bio.scipy.org Wanted List
- Go through articles in cookbook, programming guide, and tutorials sections adding links, and fixing spelling/grammar errors.
- To blog or not to blog, that is thy question? (i.e. setup a bip community blog)?
- Setup code review page with information on how we will do code reviews for the community.
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Misc Wanted List
Anything that doesn't fit anywhere else... although feel free to create new wanted lists.
