From thomas.f.hahn2 at gmail.com Sun Jan 4 04:57:27 2015 From: thomas.f.hahn2 at gmail.com (thomas hahn) Date: Sun, 04 Jan 2015 03:57:27 -0000 Subject: [EuroSciPy] 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 Message-ID: *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.Hahn2 at 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/* *) * *Primary email: **Thomas.F.Hahn2 at gmail.com* *Cell phone: 318 243 3940* *Office phone: 501 682 1440* *Office location: EIT 535* *Skype ID: tfh002* *Virtual Google Voice phone to reach me while logged into my email (i.e. * *Thomas.F.Hahn2 at gmail.com* *), even when having no cell phone reception, e.g. in big massive buildings: *(501) 301-4890 <%28501%29%20301-4890> *Web links: * 1) https://ualr.academia.edu/ThomasHahn 2) https://www.linkedin.com/pub/thomas-hahn/42/b29/42 3) http://facebook.com/Thomas.F.Hahn 4) https://twitter.com/Thomas_F_Hahn -------------- next part -------------- An HTML attachment was scrubbed... URL: From ralf.gommers at gmail.com Sun Jan 4 19:39:08 2015 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Sun, 04 Jan 2015 18:39:08 -0000 Subject: [EuroSciPy] Call for speakers for the first PyCon Belarus. EuroSciPy In-Reply-To: References: Message-ID: Hi Alina, Thank you for your email, and great to see another new Python conference being organized! I'm not sure you sent your message to euroscipy at python.org on purpose - this is the organizers list for the EuroSciPy conference and there aren't a lot of people reading it. If you would like to reach the scientific Python user/developer community, I suggest the following mailist lists: - numpy-discussion: http://mail.scipy.org/mailman/listinfo/numpy-discussion - scipy-user: http://mail.scipy.org/mailman/listinfo/scipy-user - Numfocus list: https://groups.google.com/forum/#!forum/numfocus Cheers, Ralf On Fri, Dec 12, 2014 at 1:49 PM, Alina Dolgikh wrote: > Hello, dear community! > > I represent Belarusian Python community. We have regular monthly meet-ups > for 70-100 persons and we are going to develop further. > > We are planning to make the first Belarusian PyCon on the 31st of January > and looking for speakers. > > We will be glad to meet at our event speakers, which are experienced in > public talks (links for videos of public talks or for the other conferences > web-pages are preferable) and can speak at > - highload in Python > - functional style Python > - best practices on popular tools and libraries using > - data analysis > - CI, pypy, C-extensions, python performance > - Python in mobile OS (Tizen for example) > - etc. > > Organising team is ready to cover the costs for the road and accommodation > for interested speakers. > > Thanks in advance and, please, send your responses or recommendations to > *alina at dev.by * > > Regards, > Alina Dolgikh, > PyCon > Minsk > > > _______________________________________________ > EuroSciPy mailing list > EuroSciPy at python.org > https://mail.python.org/mailman/listinfo/euroscipy > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From alina at eventspace.by Mon Jan 5 09:13:36 2015 From: alina at eventspace.by (Alina Dolgikh) Date: Mon, 05 Jan 2015 08:13:36 -0000 Subject: [EuroSciPy] Call for speakers for the first PyCon Belarus. EuroSciPy In-Reply-To: References: Message-ID: Hi, Ralf! Thanks a lot for your help! Regards, Alina On Sun, Jan 4, 2015 at 9:39 PM, Ralf Gommers wrote: > Hi Alina, > > Thank you for your email, and great to see another new Python conference > being organized! > > I'm not sure you sent your message to euroscipy at python.org on purpose - > this is the organizers list for the EuroSciPy conference and there aren't a > lot of people reading it. If you would like to reach the scientific Python > user/developer community, I suggest the following mailist lists: > > - numpy-discussion: > http://mail.scipy.org/mailman/listinfo/numpy-discussion > - scipy-user: http://mail.scipy.org/mailman/listinfo/scipy-user > - Numfocus list: https://groups.google.com/forum/#!forum/numfocus > > Cheers, > Ralf > > > > On Fri, Dec 12, 2014 at 1:49 PM, Alina Dolgikh wrote: > >> Hello, dear community! >> >> I represent Belarusian Python community. We have regular monthly meet-ups >> for 70-100 persons and we are going to develop further. >> >> We are planning to make the first Belarusian PyCon on the 31st of January >> and looking for speakers. >> >> We will be glad to meet at our event speakers, which are experienced in >> public talks (links for videos of public talks or for the other conferences >> web-pages are preferable) and can speak at >> - highload in Python >> - functional style Python >> - best practices on popular tools and libraries using >> - data analysis >> - CI, pypy, C-extensions, python performance >> - Python in mobile OS (Tizen for example) >> - etc. >> >> Organising team is ready to cover the costs for the road and >> accommodation for interested speakers. >> >> Thanks in advance and, please, send your responses or recommendations to >> *alina at dev.by * >> >> Regards, >> Alina Dolgikh, >> PyCon >> Minsk >> >> >> _______________________________________________ >> EuroSciPy mailing list >> EuroSciPy at python.org >> https://mail.python.org/mailman/listinfo/euroscipy >> >> > -------------- next part -------------- An HTML attachment was scrubbed... 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