[portland] up for tutoring anyone?

[Chris McDonald]

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 <a.m.brookins at gmail.com> 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
>> Portland at python.org
>> 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
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