From brianhray at gmail.com Tue Jan 6 00:50:30 2015 From: brianhray at gmail.com (Brian Ray) Date: Mon, 5 Jan 2015 17:50:30 -0600 Subject: [ChiPy-announce] [ANN] Best Ever Meeting this Thurs Message-ID: Overall, those who took the mentorship program surveys gave an average of 9/10 stars. There will be a Starbucks gift card for one of those who were picked presented during the meeting. This month's topics are talks from those who participated in this program. There will be a prize for the best presentation. The line up is below. This will be a very great meeting. Perhaps... our best ever. Seriously folks, don't miss this one. RSVP now... RSVP http://www.chipy.org/ and/or http://www.meetup.com/_ChiPy_/ Thank you very much for Braintree for sponsoring the food at meeting. Thanks SPACE by Doejo for hosting. Next Meeting *When:* Jan. 8, 2015, 7 p.m. *Where:* SPACE by Doejo 444 N. Wabash, 5th Floor Chicago IL Talks from Mentorship Program - *Python Mentors Lightning Talk ? Chris & Rahul* (0:07:00 Minutes) By: Chris Foresman Chris and Rahul would be talking about making RESTful API with Python. Chris was an Associate Writer at Ars Technica and is currently a Senior Systems Engineer at Vokal. Rahul is pursuing his MS in Computer Science at Illinois Institute of Technology. Chris is @foresmac on Twitter and Rahul can be reached at https://www.linkedin.com/in/rahul013k - *Example app using Flask and pg8000 (Postgres) on Heroku* (0:07:00 Minutes) By: Tanya Schlusser We walk through the architecture, development process, and a few gotchas of deploying a web application on Heroku using their free Postgresql instance, and the Python libraries 'flask' and 'pg8000' - *MM - Japhy/Sebastian - Mining and charting* (0:07:00 Minutes) By: Japhy Bartlett We'll go over how to set up a daemon for mining public data using tornado, then loading that data into some web based charts. - *ChiPy Mentorship 7-Minute Retrospective* (0:07:00 Minutes) By: Paul Ebreo Tom Yarrish and Paul Ebreo will talk about their experience of the 12 week mentorship program. They will talk about what went well and what went not-so well. They will share what they learned and give tips and tricks for a successful mentor/mentee relationship. Paul is very passionate about programming, software testing, open hardware and teaching and Tom is a Digital Forensic Analyst and teaches at Loyola University. - *Python Data Science 101 - how mentoring helped me get from raw data to SKLearn by Ben Reid* (0:07:00 Minutes) By: Ben Reid Ben will be talking about his experience getting started with Python Data Science using pandas and sci-kit learn, with Don's assistance, via the Chipy mentoring pilot program. Don is an Independent Technology Consultant, iPhone Developer and Software Architect and currently consulting with clients using Hadoop. Ben is a Senior Business Development Manager at Orbitz Worldwide and is a self taught programmer. Don is @dondrake on Twitter and Ben can be reached at https://www.linkedin.com/in/reidbenj - *Being A Mentee In The ChiPy Mentorship* By: Zachary Kerr Mentors can be incredibly valuable in helping understand software. I want to share some of the insights I have learned from my mentorship. I believe there are important lessons to be learned from mentors that can make programming a much better experience. -- Brian Ray @brianray (773) 669-7717 -------------- next part -------------- An HTML attachment was scrubbed... URL: From brianhray at gmail.com Sun Jan 18 17:22:50 2015 From: brianhray at gmail.com (Brian Ray) Date: Sun, 18 Jan 2015 10:22:50 -0600 Subject: [ChiPy-announce] [ANN] (rescheduled) January meeting this Wed Message-ID: Come listen to some amazing Python presentations from our famed mentorship program that completed this new years. Hear how you can get involved with the next batch. There will be food, drink, prizes, and lots of Python. All are welcome. No prior programming experience required. This is next Wednesday (21st) as we had to re-schedule early this month due to the End of the World. Now we see the world has not ending, we are save to come out from under our laptops and have our best meeting ever. RSVP: http://www.chipy.org/ and/or http://www.meetup.com/_ChiPy_/events/219814888/ We also have a new venue: TEK Systems 111 N Canal St Ste 105, Chicago, IL - *Example app using Flask and pg8000 (Postgres) on Heroku* (0:07:00 Minutes) By: Tanya Schlusser We walk through the architecture, development process, and a few gotchas of deploying a web application on Heroku using their free Postgresql instance, and the Python libraries 'flask' and 'pg8000' - *MM - Japhy/Sebastian - Mining and charting* (0:07:00 Minutes) By: Japhy Bartlett We'll go over how to set up a daemon for mining public data using tornado, then loading that data into some web based charts. - *ChiPy Mentorship 7-Minute Retrospective* (0:07:00 Minutes) By: Paul Ebreo Tom Yarrish and Paul Ebreo will talk about their experience of the 12 week mentorship program. They will talk about what went well and what went not-so well. They will share what they learned and give tips and tricks for a successful mentor/mentee relationship. Paul is very passionate about programming, software testing, open hardware and teaching and Tom is a Digital Forensic Analyst and teaches at Loyola University. - *Python Data Science 101 - how mentoring helped me get from raw data to SKLearn by Ben Reid* (0:07:00 Minutes) By: Ben Reid Ben will be talking about his experience getting started with Python Data Science using pandas and sci-kit learn, with Don's assistance, via the Chipy mentoring pilot program. Don is an Independent Technology Consultant, iPhone Developer and Software Architect and currently consulting with clients using Hadoop. Ben is a Senior Business Development Manager at Orbitz Worldwide and is a self taught programmer. Don is @dondrake on Twitter and Ben can be reached at https://www.linkedin.com/in/reidbenj - *Being A Mentee In The ChiPy Mentorship* By: Zachary Kerr Mentors can be incredibly valuable in helping understand software. I want to share some of the insights I have learned from my mentorship. I believe there are important lessons to be learned from mentors that can make programming a much better experience. - *Python Mentors Lightning Talk ? Chris & Rahul* (0:07:00 Minutes) By: Chris Foresman Chris and Rahul would be talking about making RESTful API with Python. Chris was an Associate Writer at Ars Technica and is currently a Senior Systems Engineer at Vokal. Rahul is pursuing his MS in Computer Science at Illinois Institute of Technology. Chris is @foresmac on Twitter and Rahul can be reached at https://www.linkedin.com/in/rahul013k -- Brian Ray @brianray (773) 669-7717 -------------- next part -------------- An HTML attachment was scrubbed... URL: From thomas.f.hahn2 at gmail.com Sun Jan 4 05:06:03 2015 From: thomas.f.hahn2 at gmail.com (thomas hahn) Date: Sun, 04 Jan 2015 04:06:03 -0000 Subject: [ChiPy-announce] 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: