From thomas.f.hahn2 at gmail.com Sun Jan 4 04:48:56 2015 From: thomas.f.hahn2 at gmail.com (thomas hahn) Date: Sat, 3 Jan 2015 21:48:56 -0600 Subject: [DB-SIG] 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 phd at phdru.name Tue Jan 6 16:54:12 2015 From: phd at phdru.name (Oleg Broytman) Date: Tue, 6 Jan 2015 16:54:12 +0100 Subject: [DB-SIG] SQLObject 2.1.0 Message-ID: <20150106155412.GA26037@phdru.name> Hello! I'm pleased to announce version 2.1.0, the first stable release of branch 2.1 of SQLObject. What's new in SQLObject ======================= Minor features -------------- * In queries generated with SQLObject's tables columns are sorted in the order they are declared in the table. * In queries generated with sqlbuilder's Insert/Update, if values are passed using dictionaries, columns are sorted alphabetically. * Tables in SELECT...FROM clause are sorted alphabetically. * MySQLConnection, PostgresConnection and SQLiteConnection have got a new method listDatabases() that lists databases in the connection and returns a list of names. * MySQLConnection, PostgresConnection and SQLiteConnection have got a new method listTables() that returns a list of table names in the database. Contributor for this release is Ian Cordasco. For a more complete list, please see the news: http://sqlobject.org/News.html What is SQLObject ================= SQLObject is an object-relational mapper. Your database tables are described as classes, and rows are instances of those classes. SQLObject is meant to be easy to use and quick to get started with. SQLObject supports a number of backends: MySQL, PostgreSQL, SQLite, Firebird, Sybase, MSSQL and MaxDB (also known as SAPDB). Python 2.6 or 2.7 is required. Where is SQLObject ================== Site: http://sqlobject.org Development: http://sqlobject.org/devel/ Mailing list: https://lists.sourceforge.net/mailman/listinfo/sqlobject-discuss Archives: http://news.gmane.org/gmane.comp.python.sqlobject Download: https://pypi.python.org/pypi/SQLObject/2.1.0 News and changes: http://sqlobject.org/News.html Oleg. -- Oleg Broytman http://phdru.name/ phd at phdru.name Programmers don't die, they just GOSUB without RETURN.