From thomas.f.hahn2 at gmail.com Sun Jan 4 05:12:29 2015 From: thomas.f.hahn2 at gmail.com (thomas hahn) Date: Sat, 3 Jan 2015 22:12:29 -0600 Subject: [melbourne-pug] 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 javier at candeira.com Thu Jan 8 06:52:54 2015 From: javier at candeira.com (Javier Candeira) Date: Thu, 8 Jan 2015 16:52:54 +1100 Subject: [melbourne-pug] Tool for capturing BOM radar as animated gif? Message-ID: Hi Melbourne pythonistas, happy New Year and apologies in advance for the potentially offtopic question. I know the BOM radar image *isn't* an animated gif, but is there a tool in the wild that will capture and export it as a gif? Bonus: it's not off topic if the tool is in Python, but obviously I'm agnostic enough to accept something written in PHP or whatever. Asking for a friend... J From dave at hopest.net Thu Jan 8 07:09:10 2015 From: dave at hopest.net (Dave Collins) Date: Thu, 08 Jan 2015 17:09:10 +1100 Subject: [melbourne-pug] Tool for capturing BOM radar as animated gif? In-Reply-To: References: Message-ID: <1420697350.21123.3.camel@gfedev21.bom.gov.au> Javier, This is not a animated gif ... however your friend might like http://www.theweatherchaser.com/radar-loop/IDR023-melbourne As for a script... well the one I have is part of product internal to the BOM. Sorry dave On Thu, 2015-01-08 at 16:52 +1100, Javier Candeira wrote: > Hi Melbourne pythonistas, happy New Year and apologies in advance for > the potentially offtopic question. > > I know the BOM radar image *isn't* an animated gif, but is there a > tool in the wild that will capture and export it as a gif? > > Bonus: it's not off topic if the tool is in Python, but obviously I'm > agnostic enough to accept something written in PHP or whatever. > > Asking for a friend... > > J > _______________________________________________ > melbourne-pug mailing list > melbourne-pug at python.org > https://mail.python.org/mailman/listinfo/melbourne-pug From krshackleton at gmail.com Thu Jan 8 07:51:51 2015 From: krshackleton at gmail.com (Kevin Shackleton) Date: Thu, 8 Jan 2015 14:51:51 +0800 Subject: [melbourne-pug] Tool for capturing BOM radar as animated gif? In-Reply-To: References: Message-ID: Hi, I wrote to BOM some years ago to ask them if they could produce an 'integrated' radar image each 24 hours - each pixel would be a normalised sum of the pixel values. This would show the path of storm events and allow farmers to see (an estimate of) which parts of their property received more rain than other parts, without having to spend the whole day watching the images. Regrettably they declined this opportunity. But perhaps they might if asked nicely package a 24-hour GIF for us all? (this would be half way to a single summed image) Although they are probably undergoing a nasty treatment of Abbott's All Purpose Elixir at present, it may catch their imagination. You never know unless you ask! Regards, Kevin. On 8 January 2015 at 13:52, Javier Candeira wrote: > Hi Melbourne pythonistas, happy New Year and apologies in advance for > the potentially offtopic question. > > I know the BOM radar image *isn't* an animated gif, but is there a > tool in the wild that will capture and export it as a gif? > > Bonus: it's not off topic if the tool is in Python, but obviously I'm > agnostic enough to accept something written in PHP or whatever. > > Asking for a friend... > > J > _______________________________________________ > melbourne-pug mailing list > melbourne-pug at python.org > https://mail.python.org/mailman/listinfo/melbourne-pug > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dave at hopest.net Thu Jan 8 23:54:31 2015 From: dave at hopest.net (Dave Collins) Date: Fri, 09 Jan 2015 09:54:31 +1100 Subject: [melbourne-pug] Tool for capturing BOM radar as animated gif? In-Reply-To: References: Message-ID: <1420757671.18583.2.camel@gfedev21.bom.gov.au> Kevin, There are rainfields products for some radars .... http://www.bom.gov.au/products/IDR02D.loop.shtml On Thu, 2015-01-08 at 14:51 +0800, Kevin Shackleton wrote: > Hi, > > > I wrote to BOM some years ago to ask them if they could produce an > 'integrated' radar image each 24 hours - each pixel would be a > normalised sum of the pixel values. > > > This would show the path of storm events and allow farmers to see (an > estimate of) which parts of their property received more rain than > other parts, without having to spend the whole day watching the > images. > > > Regrettably they declined this opportunity. But perhaps they might if > asked nicely package a 24-hour GIF for us all? (this would be half > way to a single summed image) > > > Although they are probably undergoing a nasty treatment of Abbott's > All Purpose Elixir at present, it may catch their imagination. You > never know unless you ask! > > > Regards, > > Kevin. > > > On 8 January 2015 at 13:52, Javier Candeira > wrote: > Hi Melbourne pythonistas, happy New Year and apologies in > advance for > the potentially offtopic question. > > I know the BOM radar image *isn't* an animated gif, but is > there a > tool in the wild that will capture and export it as a gif? > > Bonus: it's not off topic if the tool is in Python, but > obviously I'm > agnostic enough to accept something written in PHP or > whatever. > > Asking for a friend... > > J > _______________________________________________ > melbourne-pug mailing list > melbourne-pug at python.org > https://mail.python.org/mailman/listinfo/melbourne-pug > > > _______________________________________________ > melbourne-pug mailing list > melbourne-pug at python.org > https://mail.python.org/mailman/listinfo/melbourne-pug From peter.davis8 at gmail.com Fri Jan 9 03:48:09 2015 From: peter.davis8 at gmail.com (Peter Davis) Date: Fri, 9 Jan 2015 13:48:09 +1100 Subject: [melbourne-pug] Tool for capturing BOM radar as animated gif? In-Reply-To: <1420757671.18583.2.camel@gfedev21.bom.gov.au> References: <1420757671.18583.2.camel@gfedev21.bom.gov.au> Message-ID: My script seems to turn most radars into an animated gif. It uses ImageMagick for the final animated gif creation, I just couldn't get PIL to generate animated gifs. Testing consists of the "Works on my machine" certification, so good luck. https://gist.github.com/mrmagooey/fc22e9165d62b3ab358f On Fri, Jan 9, 2015 at 9:54 AM, Dave Collins wrote: > Kevin, > There are rainfields products for some radars .... > http://www.bom.gov.au/products/IDR02D.loop.shtml > > On Thu, 2015-01-08 at 14:51 +0800, Kevin Shackleton wrote: > > Hi, > > > > > > I wrote to BOM some years ago to ask them if they could produce an > > 'integrated' radar image each 24 hours - each pixel would be a > > normalised sum of the pixel values. > > > > > > This would show the path of storm events and allow farmers to see (an > > estimate of) which parts of their property received more rain than > > other parts, without having to spend the whole day watching the > > images. > > > > > > Regrettably they declined this opportunity. But perhaps they might if > > asked nicely package a 24-hour GIF for us all? (this would be half > > way to a single summed image) > > > > > > Although they are probably undergoing a nasty treatment of Abbott's > > All Purpose Elixir at present, it may catch their imagination. You > > never know unless you ask! > > > > > > Regards, > > > > Kevin. > > > > > > On 8 January 2015 at 13:52, Javier Candeira > > wrote: > > Hi Melbourne pythonistas, happy New Year and apologies in > > advance for > > the potentially offtopic question. > > > > I know the BOM radar image *isn't* an animated gif, but is > > there a > > tool in the wild that will capture and export it as a gif? > > > > Bonus: it's not off topic if the tool is in Python, but > > obviously I'm > > agnostic enough to accept something written in PHP or > > whatever. > > > > Asking for a friend... > > > > J > > _______________________________________________ > > melbourne-pug mailing list > > melbourne-pug at python.org > > https://mail.python.org/mailman/listinfo/melbourne-pug > > > > > > _______________________________________________ > > melbourne-pug mailing list > > melbourne-pug at python.org > > https://mail.python.org/mailman/listinfo/melbourne-pug > > > _______________________________________________ > melbourne-pug mailing list > melbourne-pug at python.org > https://mail.python.org/mailman/listinfo/melbourne-pug > -------------- next part -------------- An HTML attachment was scrubbed... URL: From krshackleton at gmail.com Fri Jan 9 05:59:12 2015 From: krshackleton at gmail.com (Kevin Shackleton) Date: Fri, 9 Jan 2015 12:59:12 +0800 Subject: [melbourne-pug] Tool for capturing BOM radar as animated gif? In-Reply-To: <1420757671.18583.2.camel@gfedev21.bom.gov.au> References: <1420757671.18583.2.camel@gfedev21.bom.gov.au> Message-ID: Wow, that's what I was looking for. Why is it only on some radars (apart from the fact it never rains in Carnarvon )? Kevin On 09/01/2015 7:18 AM, "Dave Collins" wrote: > Kevin, > There are rainfields products for some radars .... > http://www.bom.gov.au/products/IDR02D.loop.shtml > > On Thu, 2015-01-08 at 14:51 +0800, Kevin Shackleton wrote: > > Hi, > > > > > > I wrote to BOM some years ago to ask them if they could produce an > > 'integrated' radar image each 24 hours - each pixel would be a > > normalised sum of the pixel values. > > > > > > This would show the path of storm events and allow farmers to see (an > > estimate of) which parts of their property received more rain than > > other parts, without having to spend the whole day watching the > > images. > > > > > > Regrettably they declined this opportunity. But perhaps they might if > > asked nicely package a 24-hour GIF for us all? (this would be half > > way to a single summed image) > > > > > > Although they are probably undergoing a nasty treatment of Abbott's > > All Purpose Elixir at present, it may catch their imagination. You > > never know unless you ask! > > > > > > Regards, > > > > Kevin. > > > > > > On 8 January 2015 at 13:52, Javier Candeira > > wrote: > > Hi Melbourne pythonistas, happy New Year and apologies in > > advance for > > the potentially offtopic question. > > > > I know the BOM radar image *isn't* an animated gif, but is > > there a > > tool in the wild that will capture and export it as a gif? > > > > Bonus: it's not off topic if the tool is in Python, but > > obviously I'm > > agnostic enough to accept something written in PHP or > > whatever. > > > > Asking for a friend... > > > > J > > _______________________________________________ > > melbourne-pug mailing list > > melbourne-pug at python.org > > https://mail.python.org/mailman/listinfo/melbourne-pug > > > > > > _______________________________________________ > > melbourne-pug mailing list > > melbourne-pug at python.org > > https://mail.python.org/mailman/listinfo/melbourne-pug > > > _______________________________________________ > melbourne-pug mailing list > melbourne-pug at python.org > https://mail.python.org/mailman/listinfo/melbourne-pug > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dave at hopest.net Tue Jan 13 01:46:56 2015 From: dave at hopest.net (Dave Collins) Date: Tue, 13 Jan 2015 11:46:56 +1100 Subject: [melbourne-pug] Tool for capturing BOM radar as animated gif? In-Reply-To: References: <1420757671.18583.2.camel@gfedev21.bom.gov.au> Message-ID: <20150113004656.GB28342@mail.hopest.net> Kevin, I do not know the reason its only availble on some radars. I *think* its due to lack of money. dave On Fri, Jan 09, 2015 at 12:59:12PM +0800, Kevin Shackleton wrote: > Wow, that's what I was looking for. Why is it only on some radars (apart > from the fact it never rains in Carnarvon )? > > Kevin > On 09/01/2015 7:18 AM, "Dave Collins" wrote: > > > Kevin, > > There are rainfields products for some radars .... > > http://www.bom.gov.au/products/IDR02D.loop.shtml > > > > On Thu, 2015-01-08 at 14:51 +0800, Kevin Shackleton wrote: > > > Hi, > > > > > > > > > I wrote to BOM some years ago to ask them if they could produce an > > > 'integrated' radar image each 24 hours - each pixel would be a > > > normalised sum of the pixel values. > > > > > > > > > This would show the path of storm events and allow farmers to see (an > > > estimate of) which parts of their property received more rain than > > > other parts, without having to spend the whole day watching the > > > images. > > > > > > > > > Regrettably they declined this opportunity. But perhaps they might if > > > asked nicely package a 24-hour GIF for us all? (this would be half > > > way to a single summed image) > > > > > > > > > Although they are probably undergoing a nasty treatment of Abbott's > > > All Purpose Elixir at present, it may catch their imagination. You > > > never know unless you ask! > > > > > > > > > Regards, > > > > > > Kevin. > > > > > > > > > On 8 January 2015 at 13:52, Javier Candeira > > > wrote: > > > Hi Melbourne pythonistas, happy New Year and apologies in > > > advance for > > > the potentially offtopic question. > > > > > > I know the BOM radar image *isn't* an animated gif, but is > > > there a > > > tool in the wild that will capture and export it as a gif? > > > > > > Bonus: it's not off topic if the tool is in Python, but > > > obviously I'm > > > agnostic enough to accept something written in PHP or > > > whatever. > > > > > > Asking for a friend... > > > > > > J > > > _______________________________________________ > > > melbourne-pug mailing list > > > melbourne-pug at python.org > > > https://mail.python.org/mailman/listinfo/melbourne-pug > > > > > > > > > _______________________________________________ > > > melbourne-pug mailing list > > > melbourne-pug at python.org > > > https://mail.python.org/mailman/listinfo/melbourne-pug > > > > > > _______________________________________________ > > melbourne-pug mailing list > > melbourne-pug at python.org > > https://mail.python.org/mailman/listinfo/melbourne-pug > > > _______________________________________________ > melbourne-pug mailing list > melbourne-pug at python.org > https://mail.python.org/mailman/listinfo/melbourne-pug From lex.lists at gmail.com Mon Jan 19 06:59:20 2015 From: lex.lists at gmail.com (Lex H) Date: Mon, 19 Jan 2015 16:59:20 +1100 Subject: [melbourne-pug] [JOB] Mid-Level Python dev role. Message-ID: Hi, Company I work for are currently hiring a Python dev [our last hire came from this list ;) ] As far as experience goes we're looking for a mid-level developer to an experienced junior. Get to work with some interesting tech. In the past 12 months you would likely have worked with: * Python * Django * Riak * Git * AWS * SaltStack * RethinkDB * Pandas * ... Role isn't your traditional webapp building role. Job ad here: https://www.linkedin.com/jobs2/view/40786962 If you're interested send me your details to: lex+cv at jbadigital.com Cheers, Lex. -------------- next part -------------- An HTML attachment was scrubbed... URL: