Help with finding tutors for Python, Linux, R, Perl, Octave, MATLAB and/or Cytoscape for yeast microarray analysis, next generation sequencing and constructing gene interaction networks
*Help with finding tutors for Python, Linux, R, Perl, Octave, MATLAB and/or Cytoscape for yeast microarray analysis, next generation sequencing and constructing gene interaction networks* Hi I am a visually impaired bioinformatics graduate student using microarray data for my master’s thesis aimed at deciphering the mechanism by which the yeast wild type can suppress the rise of free reactive oxygen species (ROS) induced by caloric restriction (CR) but the Atg15 and Erg6 knockout mutant cannot. Since my remaining vision is very limited I need very high magnification. But that makes my visual field very small. Therefore I need somebody to teach me how to use these programming environments, especially for microarray analysis, next generation sequencing and constructing gene and pathway interaction networks. This is very difficult for me to figure out without assistance because Zoomtext, my magnification and text to speech software, on which I am depending because I am almost blind, has problems reading out aloud many programming related websites to me. And even those websites it can read, it can only read sequentially from left to right and then from top to bottom. Unfortunately, this way of acquiring, finding, selecting and processing new information and answering questions is too tiresome, exhausting, ineffective and especially way too time consuming for graduating with a PhD in bioinformatics before my funding runs out despite being severely limited by my visual disability. I would also need help with writing a good literature review and applying the described techniques to my own yeast Affimetrix microarray dataset because I cannot see well enough to find all relevant publications on my own. Some examples for specific tasks I urgently need help with are: 1.Analyzing and comparing the three publically available microarray datasets that can be accessed at: A.http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE41860 B.http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38635 C. http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9217 2.Learning how to use the Affymetrics microarray analysis software for the Yeast 2 chip, which can be found at http://www.affymetrix.com/support/technical/libraryfilesmain.affx 3.For Cytoscape I need somebody, who can teach me how to execute the tutorials at the following links because due to my very limited vision field I cannot see tutorial and program interface simultaneously. A. http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Introduction_to_Cytoscape_3.1-part2#Importing_and_Exploring_Your_Data B. http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Filtering_and_Editing_in_Cytoscape_3 C. http://cytoscape.org/manual/Cytoscape2_8Manual.html#Import%20Fixed-Format%20Network%20Files D. http://wiki.cytoscape.org/Cytoscape_User_Manual/Network_Formats 4.Learning how to use the TopGo R package to perform statistical analysis on GO enrichments. Since I am legally blind the rehab agency is giving me money to pay tutors for this purpose. Could you please help me getting in touch regarding this with anybody, who could potentially be interested in teaching me one on one thus saving me time for acquiring new information and skills, which I need to finish my thesis on time, so that I can remain eligible for funding to continue in my bioinformatics PhD program despite being almost blind? The tutoring can be done remotely via TeamViewer 5 and Skype. Hence, it does not matter where my tutors are physically located. Currently I have tutors in Croatia and UK. But since they both work full time jobs while working on their PhD dissertation they only have very limited time to teach me online. Could you therefore please forward this request for help to anybody, who could potentially be interested or, who could connect me to somebody, who might be, because my graduation and career depend on it? Who else would you recommend me to contact regarding this? Where else could I post this because I am in urgent need for help? Could you please contact me directly via email at thomas.f.ha...@gmail.com and/or Skype at tfh002 because my text to speech software has problems to read out this website aloud to me? I thank you very much in advance for your thoughts, ideas, suggestions, recommendations, time, help, efforts and support. With very warm regards, *Thomas Hahn* 1)*Graduate student in the Joint Bioinformatics Program at the University of Arkansas at Little Rock (UALR) and the University of Arkansas Medical Sciences (UAMS) * 2)*Research Industry Advocate, Founder and Board Member of RADISH MEDICAL SOLUTIONS, INC. (**http://www.radishmedical.com/thomas-hahn/* http://www.radishmedical.com/thomas-hahn/*) * *Primary email: **thomas.f.ha...@gmail.com* thomas.f.ha...@gmail.com *Cell phone: 318 243 3940* *Office phone: 501 682 1440* *Office location: EIT 535* *Skype ID: tfh002* *Virtual Google Voice
Re: Help with finding tutors for Python, Linux, R, Perl, Octave, MATLAB and/or Cytoscape for yeast microarray analysis, next generation sequencing and constructing gene interaction networks
On Sunday, January 4, 2015 8:45:08 AM UTC+5:30, thomas hahn wrote: Help with finding tutors for Python, Linux, R, Perl, Octave, MATLAB and/or Cytoscape for yeast microarray analysis, next generation sequencing and constructing gene interaction networks Hi Thomas This is a reasonably friendly and generally knowledgeable place for python related questions. Feel free to ask your questions here. If you need help starting programming and python is your chosen medium there is also a tutors list https://mail.python.org/mailman/listinfo/tutor. As for the rest... Have a vague idea what yeast is None whatever of cytospace And probably think a 'microarray' other than what you do [That was a joke. More seriously...] Specialized areas of application of python are less likely to find help out here That being the case, starting out with python needs a focussed approach - Spend a few days getting into python - Then worry about applying it to your needs In your case you are not just starting python but python perl R octave mathlab linux In this manner you are setting yourself up for failure unless you have enough money to hire people for all your programming work. I can tell you that python ecosystem can offer most of what perl, R, octave mathlab offer. But for that you have to go beyond core python to things like scipy, pandas etc. Fans of perl, R, octave, mathlab will tell you the same for these as well You may want to start by throwing a 5-sided coin. Best wishes on your studies Rusi -- https://mail.python.org/mailman/listinfo/python-list
[issue23159] argparse: Provide equivalent of optparse.OptionParser.{option_groups, option_list, get_option}
New submission from Eric McDonald:
There are several use cases for having the equivalent of the
optparse.OptionParser 'get_option' method and the 'option_groups' and
'option_list' properties in argparse.ArgumentParser class.
(1) Easy alteration of the text of the default help option. With optparse, one
could write:
oparser.get_option( -h ).help
'show this help message and exit'
oparser.get_option( -h ).help = Show this help message and exit.
oparser.get_option( -h ).help
'Show this help message and exit.'
The equivalent facility does not appear to exist in argparse. (Issue #19462,
http://bugs.python.org/issue19462, is about a different use case. And, while
https://docs.python.org/3/library/argparse.html#add-help suggests a workaround
with add_help=False and then creating a new option with the 'help' action, it
is still less convenient than altering the existing help option.)
(2) Inspection of all the argument declarations in an ArgumentParser object
after it has been populated. This is particularly useful if you want to look
for the equivalent of the available options in config files and don't want to
have write explicit code which separately enumerates the available config file
keys and how to handle them. With an OptionParser, one could use the
'option_groups' attribute to find all option groups (to correspond to config
file sections) and the 'option_list' attribute to find all options (to
correspond to config file keys); these are all part of the published interface
and provide relatively simple data types to inspect. With an Argument Parser,
one needs to rely upon the unpublished interface (the '_actions' attribute of a
parser, etc...).
--
components: Library (Lib)
messages: 233394
nosy: emcd
priority: normal
severity: normal
status: open
title: argparse: Provide equivalent of
optparse.OptionParser.{option_groups,option_list,get_option}
type: enhancement
versions: Python 3.5
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Re: list comparison vs integer comparison, which is more efficient?
On 1/3/2015 6:19 PM, austin aigbe wrote: I am currently implementing the LTE physical layer in Python (ver 2.7.7). For the qpsk, 16qam and 64qam modulation I would like to know which is more efficient to use, between an integer comparison and a list comparison: Integer comparison: bit_pair as an integer value before comparison # QPSK - TS 36.211 V12.2.0, section 7.1.2, Table 7.1.2-1 def mp_qpsk(self): r = [] for i in range(self.nbits/2): bit_pair = (self.sbits[i*2] 1) | self.sbits[i*2+1] if bit_pair == 0: r.append(complex(1/math.sqrt(2),1/math.sqrt(2))) elif bit_pair == 1: r.append(complex(1/math.sqrt(2),-1/math.sqrt(2))) elif bit_pair == 2: r.append(complex(-1/math.sqrt(2),1/math.sqrt(2))) elif bit_pair == 3: r.append(complex(-1/math.sqrt(2),-1/math.sqrt(2))) return r List comparison: bit_pair as a list before comparison # QPSK - TS 36.211 V12.2.0, section 7.1.2, Table 7.1.2-1 def mp_qpsk(self): r = [] for i in range(self.nbits/2): bit_pair = self.sbits[i*2:i*2+2] if bit_pair == [0,0]: r.append() elif bit_pair == [0,1]: r.append(complex(1/math.sqrt(2),-1/math.sqrt(2))) elif bit_pair == [1,0]: r.append(complex(-1/math.sqrt(2),1/math.sqrt(2))) elif bit_pair == [1,1]: r.append(complex(-1/math.sqrt(2),-1/math.sqrt(2))) return r Wrong question. If you are worried about efficiency, factor out all repeated calculation of constants and eliminate the multiple comparisons. sbits = self.sbits a = 1.0 / math.sqrt(2) b = -a points = (complex(a,a), complex(a,b), complex(b,a), complex(b,b)) complex(math.sqrt(2),1/math.sqrt(2)) def mp_qpsk(self): r = [points[sbits[i]*2 + sbits[i+1]] for i in range(0, self.nbits, 2)] return r -- Terry Jan Reedy -- https://mail.python.org/mailman/listinfo/python-list
[issue23160] Respect the environment variable SVNROOT in external-common.bat
New submission from Anselm Kruis: Issue #21907 introduced the environment variable SVNROOT in PCbuild/get_externals.bat. I propose to use the same variable in Tools/buildbot/external-common.bat too. This batch contains many verbatim copies of the SVN-URL. With the provided patch, it would become much simpler to use a (local) mirror of svn.python.org. -- components: Build messages: 233395 nosy: anselm.kruis priority: normal severity: normal status: open title: Respect the environment variable SVNROOT in external-common.bat type: enhancement versions: Python 2.7, Python 3.4 ___ Python tracker rep...@bugs.python.org http://bugs.python.org/issue23160 ___ ___ Python-bugs-list mailing list Unsubscribe: https://mail.python.org/mailman/options/python-bugs-list/archive%40mail-archive.com
[issue23160] Respect the environment variable SVNROOT in external-common.bat
Anselm Kruis added the comment: Patch for 3.4 -- keywords: +patch Added file: http://bugs.python.org/file37593/issue23160-3.4.diff ___ Python tracker rep...@bugs.python.org http://bugs.python.org/issue23160 ___ ___ Python-bugs-list mailing list Unsubscribe: https://mail.python.org/mailman/options/python-bugs-list/archive%40mail-archive.com
[issue23160] Respect the environment variable SVNROOT in external-common.bat
Anselm Kruis added the comment: Patch for 2.7 -- nosy: +zach.ware Added file: http://bugs.python.org/file37594/issue23160-2.7.diff ___ Python tracker rep...@bugs.python.org http://bugs.python.org/issue23160 ___ ___ Python-bugs-list mailing list Unsubscribe: https://mail.python.org/mailman/options/python-bugs-list/archive%40mail-archive.com
[issue23161] collections.abc.MutableSet missing methods
New submission from Devin Jeanpierre:
set(dir(set)) - set(dir(collections.abc.MutableSet))
{'copy', 'update', '__rsub__', 'union', 'issubset', 'intersection',
'issuperset', '__rxor__', 'difference', 'symmetric_difference',
'difference_update', '__rand__', 'intersection_update',
'symmetric_difference_update', '__ror__'}
Most of these should be implemented on MutableSet rather than subclasses.
--
messages: 233398
nosy: Devin Jeanpierre
priority: normal
severity: normal
status: open
title: collections.abc.MutableSet missing methods
versions: Python 3.4
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[issue23161] collections.abc.MutableSet missing methods
Changes by Devin Jeanpierre jeanpierr...@gmail.com: -- components: +Library (Lib) ___ Python tracker rep...@bugs.python.org http://bugs.python.org/issue23161 ___ ___ Python-bugs-list mailing list Unsubscribe: https://mail.python.org/mailman/options/python-bugs-list/archive%40mail-archive.com
