tag:blogger.com,1999:blog-6363246379112249261.post8772951458735279346..comments2023-06-28T12:01:24.462-04:00Comments on It's Not Easy Being Genes: Not the Biopythonista I thought I'd beAnonymoushttp://www.blogger.com/profile/01078483442220289712noreply@blogger.comBlogger6125tag:blogger.com,1999:blog-6363246379112249261.post-42067833775361399972009-02-05T07:03:00.000-05:002009-02-05T07:03:00.000-05:00I recognize myself in everything you said and in t...I recognize myself in everything you said and in the comments above.<BR/><BR/>I have tried to propose a template for tests and file parsers that could be used by newbies, but they seem to don't care.<BR/>Too bad..<BR/><BR/>- http://bugzilla.open-bio.org/show_bug.cgi?id=2749Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-6363246379112249261.post-7813882603371000842008-09-14T21:41:00.000-04:002008-09-14T21:41:00.000-04:00I agree with the post above. I have had ideas abou...I agree with the post above. I have had ideas about getting involved with the biopython community and my stumbling block comes the fact of being unable to pursue anything I can find to be meaningful. I am newbie interested in developing my biopython skills by learning about the project and contributing in anyway I can. But I just cannot find anything I can do at a newbie level. It would be really nice if things could be assigned to people according to their skillsets. For one I think biopython has awful documentation. Someone should really need to work on that. But exactly what? I wish someone would lay down the guidelines so others can pick up. I find that kind of community sense sadly lacking in biopython. Just my 2 cents.Quantrixhttps://www.blogger.com/profile/17004885355658343077noreply@blogger.comtag:blogger.com,1999:blog-6363246379112249261.post-42980602545178262882008-08-20T00:05:00.000-04:002008-08-20T00:05:00.000-04:00I had/have the same aspirations of being neck deep...I had/have the same aspirations of being neck deep in biopython in the closing days as an undergrad in bioinformatics. I start my third year as an undergrad on monday and still feel like I can't code my way out of a paper bag, at least not without a bunch of helper code. Looking back toward your days as an undergrad what would you have done differently?Rickhttps://www.blogger.com/profile/08325242096187696153noreply@blogger.comtag:blogger.com,1999:blog-6363246379112249261.post-84552750963188074492008-08-13T16:54:00.000-04:002008-08-13T16:54:00.000-04:00@Andrew Thanks so much for your thoughtful comment...@Andrew Thanks so much for your thoughtful comments. That's interesting about your AAIndex parser not fitting the "Biopython style" because as far as I know, there are no style guidelines really set. And really, why should it? Standardization is something that I think will come about after a library is established, but a working library is not going to be established by setting standards.<BR/><BR/>A rejuvenation project is a good idea. Again, how can we do this? It takes time and it really would help knowing what is <I>already</I> in the library, and what <I>isn't</I> and is critically missing. It takes a lot of users probably to get an idea of both of those, particularly the latter. I had a thought of documenting a Biopython module a month. I wonder if this would be a feasible project.<BR/><BR/>I think I will solicit the Biopython and Biology in Python lists for more input on this. While Titus Brown wrote <A HREF="http://ivory.idyll.org/blog/aug-08/am-i-jealous" REL="nofollow">a great blog post</A> recently on the importance of execution, I think if I could get more of us Pythonistas at least talking about this and being in contact, that's at least a start. BIP may have a meeting at the upcoming SciPy conference, too, and maybe I can convince them to make discussing this stuff a priority there.<BR/><BR/>Also, again, and as a side note, I'd like to bring up this conflict I feel in that by helping Biopython (or Biology in Python--whatever gets some cohesion in the Python bioinformatics community), I am doing more to progress science than by doing research in my own little thesis project, but I am only rewarded (read, kept on a stipend) by doing the latter. What would be fantastic is if grants existed for the purpose of building and maintaining these libraries and providing educational opportunities to life sciences. Maybe that's a pipe dream, but maybe someone with some influence on funding will read this and think this is a Good Idea™. :-)<BR/><BR/>Also, thanks for mentioning the FriendFeed thread. I love the feedback coming through there, as well.<BR/><BR/>@Deepak, I so was thinking the same thing. Haha!Anonymoushttps://www.blogger.com/profile/01078483442220289712noreply@blogger.comtag:blogger.com,1999:blog-6363246379112249261.post-27577924271286551392008-08-11T00:45:00.000-04:002008-08-11T00:45:00.000-04:00Andrew, what's this about "busty" work :). Sorry,...Andrew, what's this about "busty" work :). Sorry, couldn't resistAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-6363246379112249261.post-39485490299735882922008-08-08T22:17:00.000-04:002008-08-08T22:17:00.000-04:00(some comments on FriendFeed, some here since I co...(some <A HREF="http://friendfeed.com/e/46473e64-3a58-4608-beab-e630aa673791/Not-the-Biopythonista-I-thought-I-d-be/" REL="nofollow">comments on FriendFeed</A>, some here since I could have spammed up FriendFeed with too many comment boxes).<BR/><BR/>I also contributed a small module once (an AAIndex parser, actually).. it wasn't amazingly elegant or fully complete, but it did the job in a 'production setting' so it should have been okay. The mailinglist email was overlooked by the core Biopython devs, and it was ignored. A few months later, someone came asking for an AAIndex parser .. I emailed again, but by Iddo had already written his own implementation, which he felt fitted the "biopython-style" better, and included that instead. I'm not miffed that my code wasn't included ... this is a strength of open source ... we had *two* implementations to choose from, and the better implementation was chosen (although I can't find an AAIndex parser in the Biopython, I think it was dropped at some later stage). I guess I just feel like the project could take a few tips from <A HREF="http://producingoss.com/" REL="nofollow">Producing Open Source Software</A> by Karl Fogel.<BR/><BR/>It has crossed my mind in recent weeks that maybe a Biopython rejuvenation project would be a good idea, but I haven't been following the mailinglist, and like you, don't feel like I have time to do any of it properly alone, and knowing that the critical mass BioPerl has is lacking.<BR/><BR/>Once thing I'd like to do is survey which parts of Bioperl are actually most used (maybe just via Google Code search), and see if there are any key holes in Biopython that could be filled to help bring some parity. Are you up for a collaborative weekend of "busty work" sometime ?Anonymousnoreply@blogger.com