From thomas.f.hahn2 w gmail.com Sun Jan 4 05:17:10 2015 From: thomas.f.hahn2 w gmail.com (thomas hahn) Date: Sat, 3 Jan 2015 22:17:10 -0600 Subject: [PLPUG] 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 w 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 w 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 w 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 -------------- następna część --------- Załącznik HTML został usunięty... URL: From galuszkak w gmail.com Fri Jan 23 13:01:52 2015 From: galuszkak w gmail.com (=?UTF-8?Q?Kamil_Ga=C5=82uszka?=) Date: Fri, 23 Jan 2015 13:01:52 +0100 Subject: [PLPUG] Z FB o PyCon Belaraus Message-ID: Przeklejam info. Cześć! Organizatorzy PyCona na Białorusi poszukują uczestników oraz prelegentów. Konferencja już tuż tuż (31. stycznia), ale zapewniają sprawną pomoc w organizacji dojazdu oraz zdobycia wizy. Poniżej zamieszczam wiadomość od jednej z organizatorek. Pozdrawiam, Przemek Lewandowski ---- The first PyCon Belarus is going to be set in Minsk on the 31st of January. Everything is going to happen in a special place for the IT-events SPACE . PyCon Belarus 2015 timeline is carefully packed with traditional pythonic subjects of scaling, testing and writing web applications and extended with advanced topics of "unconventional python usage" ? functional python, static typing, automated "Java-style" refactoring and data analysis. The conference is supported by Python Software Foundation and we are happy to meet David Mertz as a keynote speaker. Our partners from Wargaming , Doist , Yandex and JetBrains share their python development best practises with the guests. Entry price is $65 for a regular ticket and $85 for VIP access. Yet today we are happy to offer a special price for all PyWaw community members. Use the link http://afisha.bycard.by/order/110577 and buy the ticket with 20% off. Organizing team is happy to help you with visa issuing. Please forward your requests to alina [at] eventspace.by, it's not too late to apply! --- Pozdrawiam Kamil Gałuszka -------------- next part -------------- An HTML attachment was scrubbed... URL: From fklebczyk w gmail.com Fri Jan 23 22:25:55 2015 From: fklebczyk w gmail.com (=?UTF-8?B?RmlsaXAgS8WCxJliY3p5aw==?=) Date: Fri, 23 Jan 2015 22:25:55 +0100 Subject: [PLPUG] =?utf-8?q?Deklaracja_cz=C5=82onkowska=2C_sk=C5=82adki=2C_?= =?utf-8?q?aktualna_wersja_statutu?= Message-ID: <54C2BC63.5000201@gmail.com> Witam, Przesyłam oficjalną informacje od Zarządu: Zajęło nam to trochę czasu, ale ruszamy mocno z kopyta. Informujemy, że jest już możliwość zapisywania się do Stowarzyszenia Polska Grupa Użytkowników Pythona dla nowych członków. Wszystkich zainteresowanych współtworzeniem polskiej społeczność Pythona, zachęcamy do zapoznania się z treścią deklaracji członkowskiej oraz statutem Stowarzyszenia PLPUG, a następnie wstępowania do naszej organizacji i udzielania się w przyszłych inicjatywach. Deklaracja zawiera na końcu opcjonalną ankietę, co pomoże nam w lepszym zrozumieniu oczekiwań co do stowarzyszenia, jak również przyczyni się poznania nowych członków. Wpłaty na konto bankowe Stowarzyszenia PLPUG będą mogłby być realizowane dopiero po założeniu konta, co nastąpi w przeciągu maksymalnie dwóch tygodni - mamy wybrany bank i w przyszłą środę podpisujemy umowę. Po oszacowaniu kosztów jakie będzie ponosić stowarzyszenie, w dniu 20 stycznia 2015 roku, Zarządu Stowarzyszenia Polska Grupa Użytkowników podjął uchwałę w sprawie wysokość i zasad płacenia składek członkowskich. Zarząd PLPUG przyjął uchwałę nr 1/2015 jednogłośnie. [1] http://plpug.org/docs/PLPUG-Deklaracja-cz%C5%82onkowska.pdf [2] https://github.com/plpug/plpug-statut [3] http://plpug.org/uchwaly/PLPUG-Uchwa%C5%82a-1-2015.pdf From fklebczyk w gmail.com Fri Jan 23 22:35:26 2015 From: fklebczyk w gmail.com (=?UTF-8?B?RmlsaXAgS8WCxJliY3p5aw==?=) Date: Fri, 23 Jan 2015 22:35:26 +0100 Subject: [PLPUG] =?utf-8?q?Deklaracja_cz=C5=82onkowska=2C_sk=C5=82adki=2C_?= =?utf-8?q?aktualna_wersja_statutu?= In-Reply-To: <54C2BC63.5000201@gmail.com> References: <54C2BC63.5000201@gmail.com> Message-ID: <54C2BE9E.1000106@gmail.com> Co do sposobu przekazywania deklaracji członkowskich to w chwili obecnej można je przesyłać na adres PLPUG: Stowarzyszenie Polska Grupa Użytkowników Pythona ul. Madalińskiego 106 02-506 Warszawa, Polska lub przekazać osobiście osobom z Zarządu: Jędrzej Nowak - Wrocław Piotr Tynecki - Białystok Piotr Skamruk - Trójmiasto Filip Kłębczyk - Katowice Pozdrawiam, Filip