I have a friend that would very likely be interested in this as well. He does a heavy amount of scientific computing but most of it is in Fortran, he is looking to move to Python eventually though and I think this would be ideal for him. I on the other hand have lots of python experience but non in the big dataset/scientific world but I can help in the same way offered by Andrew, a web developer who knows how to distribute tasks using queues and databases.
I'll ping him with regards to this and see what he thinks. -Wraithan On Thu, Oct 20, 2011 at 1:46 PM, Andrew Brookins <[email protected]> wrote: > Heather (and everyone), > > On Oct 14, 2011, at 8:22 PM, Heather Lintz wrote: > >> Hi Pythonistas, >> >> I am a Corvallis ghost member of your group. My name is Heather. I am also >> an ecologist working on climate change topics. I program all the time in >> MATLAB, and less often in R and Python. So far, I have only used Python to >> do some ArcGIS tasks using the ArcGIS library in Python (and some other >> basic libraries too). However, I now have a couple somewhat hefty new >> projects I would like to accomplish in Python. I was wondering if there is a >> good time/place to catch some of you and talk about some potential >> Python tutoring with these tasks in mind. I already have some experience >> with the language (for example, I posted some of my code below that I wrote >> awhile and forgot about). Is the monthly meet-up a good place for this? >> You seem to have agendas for those meetings perhaps? >> >> Here are the projects I have in mind that I would like to work on: >> >> 1. Code a statistical algorithm and divide and delegate computation tasks to >> multiple processors on a Linux system. The processors would each generate >> results and the results would be pooled for an optimization. >> >> 2. Import RNA Seq data generated from the Illumina High Seq 2000 and learn >> how to manipulate INSANELY large bioinformatics/genomics data sets. I >> especially like >> to do statistics on such data (things that I normally do in MATLAB). >> But this time it would be treating the INSANELY LARGE AMOUNT of data as a >> matrix to manipulate it, etc. in Python. >> >> I'd like to come up twice a month for Python 'tutoring' to get these >> projects accomplished and learn Python better. There's nothing like wisdom >> from other programmers to help. Would this interest any of you? Can you >> recommend someone in your group that is great at >> scientific-python-programming-teaching challenges? >> >> Many thanks, >> Heather >> >> >> P.s. Here's my previous dinky Python code that I already forgot about. It's >> the max of my ability. >> >> ######################## >> # Import system modules >> ######################## >> >> import sys, string, os, arcgisscripting, copy, glob, linecache, csv from >> quantile import quantile >> >> # Create the Geoprocessor >> gp = arcgisscripting.create() >> gp.overwriteoutput = 1 >> >> #################################################################### >> #READ DATA FROM EACH ASC FILE AND CALCULATE QUANTILES FROM EACH FILE >> #################################################################### >> >> q1=[] >> q2=[] >> q3=[] >> >> os.chdir(ascDIR) >> runlist=os.listdir(ascDIR) >> print repr(runlist) >> print len(runlist) >> for file in runlist: >> print repr(file) >> gq=[] >> x=open(file,'r') >> for i in xrange(6): >> x.readline() >> z= x.readline() >> while z != '': >> z=z.strip().split() >> for num in z: >> num=float(num) >> if num > -1: >> gq.append(num) >> z= x.readline() >> a=quantile(gq, .25, qtype = 7, issorted = False) >> #print a >> b=quantile(gq, .5, qtype = 7, issorted = False) >> c=quantile(gq, .75, qtype = 7, issorted = False) >> q1.append(a) >> q2.append(b) >> q3.append(c) >> print len(q1), len(q2), len(q3) >> >> outfile = open("outfile.txt", "w") >> for i in xrange(len(q1)): >> outfile.write("%12.3e%12.3e%12.3e\n" % (q1[i], q2[i], q3[i])) >> outfile.close() >> >> outfile = open("outfilezones.txt", "w") >> for i in xrange(len(q1)): >> outfile.write(runlist) >> outfile.close() >> >> >> >> _______________________________________________ >> Portland mailing list >> [email protected] >> http://mail.python.org/mailman/listinfo/portland > > This is a really awesome question. > > There are a few hack-nights around town that aren't oriented around a > specific language that you could attend. Check: http://calagator.org/ > > I'm not aware of a regular Python tutoring/workshop style meeting (maybe > someone else is). However, I would be very interested in participating in and > helping to organize such a meeting. > > As for your particular problem, I haven't done any scientific computing, but > I can share my experience using Python for web development. Maybe there is > some technology crossover (message queues, or even just your database layer? > Oops, I dunno, I'm not a scientist!). > > Anyway, "large bioinformatics/genomics data"? Sounds awesome! > > Best, > Andrew > _______________________________________________ > Portland mailing list > [email protected] > http://mail.python.org/mailman/listinfo/portland > _______________________________________________ Portland mailing list [email protected] http://mail.python.org/mailman/listinfo/portland
