From Ganesh.Shankar at RoswellPark.org Tue Jun 6 11:04:50 2006 From: Ganesh.Shankar at RoswellPark.org (Shankar, Ganesh) Date: Tue, 6 Jun 2006 14:04:50 -0400 Subject: [Buffalo-pm] Job Announcement Message-ID: <6FF91AE4F1DC7743A6466E334EB865AE0BF84C79@VERITY.roswellpark.org> Hello All, This is to announce a job opening for a Programmer in the Center of Excellence in Bioinformatics. The Center is a multidisciplinary effort between Roswell Park and UB which utilizes the skills of scientists, statisticians and computer engineers. Job Description The programmer will support the research activities of statisticians, cancer researchers and bioinformaticians. The general scientific, investigative method being used is based on microarray technology. As such, problems arise when managing and analyzing the huge data sets generated by each experiment. Description of data The raw data is tabular, with approx. 20 columns and up to 20,000 rows. These dimensions will increase but this is a good starting point. The raw data undergoes quality control checks and initial analysis before being released to the customer. Because of the nature of the experiment and the methods used to measure the results, the data are inherently noisy. Therefore, they need to be statistically normalized to "reveal" the true result. The statisticians synthesize new methods to try and do this all the time. They'll have the ideas, and the programmer will have to code it up using statistical libraries from Bioconductor or other sources. The result is usually a graph that is generated by the program. We expect the new hire to pick up the nature and reasoning of the experiment in a few months. Management of data The raw data needs to be correctly and promptly piped from the origin (the imaging machine) to a database or Laboratory Information Management System(LIMS). Data should be available to internal users and external customers. Analysis of data The raw data from the experiment needs to be analyzed. Certain standard, quality control calculations need to performed for all data and the results stored in the database or LIMS. Existing programs written in R will have to be modified to conform to Bioconductor standards and to integrate with the database or LIMS. Further non-standard, exploratory analysis algorithms will be designed by the statistical or scientific leads and will have to be implemented by the programmer. General Tasks The programmer is initially expected to implement, modify, and integrate existing algorithms, and programs. The programmer will also standardize the current infrastructure to increase compatibility and throughput. Given requirements from the scientist, the programmer should be able to design and implement a program to perform the given task with minimal supervision. The implementation should integrate or communicate with existing programs in R, Perl or Java. Specific Tasks Implement computational algorithms and statistical methods for the analysis of array comparative genomic hybridization, microarray gene expression and other high throughput datasets. Summarize, document and present results generated by the analyses of datasets. Assist in the preparation of materials for publications and grant applications. Interact with lab personnel employed by array based core resources at RPCI to facilitate a better understanding of the interplay of the underlying biological, technical, and statistical issues. Work with IT specialists to enhance the implementation of statistical methods and computational algorithms on the available computing infrastructures. Provide documentation for custom software and algorithms. Examples of Projects Develop R library of custom functions for the analysis of aCGH data. Develop custom interface for internal software and external software such as the Bioconductor library. Conduct standard analyses of array data (e.g., implement data smoothers, run SAM, run GeneDirector, run GenePix, and other software platforms). Preferred Skills Coursework in statistics and Bachelor's degree in CS with experience programming in languages such as C, C++, R, Fortran, Perl or Java or Java. Familiarity with database management systems such as Oracle, or MySQL a plus. Should be comfortable with Unix/Linux OS. Salary Commensurate with education and experience. Contact Daniel Gaile, Ph.D. Department of Biostatistics School of Public Health and Health Professions Farber Hall Rm. 249 3435 Main Street, Buffalo, NY 14214-3000 dpgaile at buffalo.edu (716) 881-8955 office (716) 909-1633 cell (716) 829-2200 FAX OR Jeffrey Miecznikowski, Ph.D. Department of Biostatistics School of Public Health and Health Professions Farber Hall Rm. 249 3435 Main Street, Buffalo, NY 14214-3000 jcm38 at buffalo.edu (716) 881-8957 office (716) 829-2200 FAX This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. From dmagnuszewski at mandtbank.com Wed Jun 14 11:35:37 2006 From: dmagnuszewski at mandtbank.com (DANIEL MAGNUSZEWSKI) Date: Wed, 14 Jun 2006 14:35:37 -0400 Subject: [Buffalo-pm] June Meeting - Randal Schwartz in Buffalo Message-ID: Mongers, I have some good news! Randal Schwartz will be in town next week and he is willing to give a talk at this month's meeting (June 20th). He has two talks for us to choose from: 1) Perl Best Practices (http://www.samag.com/documents/s=10086/sam0607h/a8.htm) 2) Inside Out Objects (http://www.samag.com/documents/s=9979/sam0603g/0603g.html) Please vote for the talk that you would like to see by replying to me via email - I will keep the tally. Seeing as the meeting is less than a week away, I ask that you reply ASAP! The voting will end around 5 PM on Friday, so that I can give him a heads up on the topic. The next meeting will be held at 7PM on June 20th, in Bell 242, UB North Campus. I will be updating the website shortly. Thanks! -Dan From dmagnuszewski at mandtbank.com Thu Jun 15 07:33:16 2006 From: dmagnuszewski at mandtbank.com (DANIEL MAGNUSZEWSKI) Date: Thu, 15 Jun 2006 10:33:16 -0400 Subject: [Buffalo-pm] Fwd: Dorm Rooms and Meal Cards Message-ID: FYI - for those going to YAPC -------------- next part -------------- An embedded message was scrubbed... From: "Joshua McAdams" Subject: Dorm Rooms and Meal Cards Date: Thu, 15 Jun 2006 10:29:45 -0400 Size: 2915 Url: http://mail.pm.org/pipermail/buffalo-pm/attachments/20060615/176098c6/attachment.mht From dmagnuszewski at mandtbank.com Fri Jun 16 12:55:59 2006 From: dmagnuszewski at mandtbank.com (DANIEL MAGNUSZEWSKI) Date: Fri, 16 Jun 2006 15:55:59 -0400 Subject: [Buffalo-pm] June Meeting - Randal Schwartz in Buffalo Message-ID: Well, there was an overwhelming response for the "Best Practices" talk (a.k.a. - no one voted for inside out objects). I just emailed Randal and let him know the decision. I think this talk will be beneficial to those at every skill level, so I'd like to encourage everyone to attend. Here's the final agenda for next Tuesday: Topic: Randal Schwartz on "Perl Best Practices" Date: Tuesday, June 20th, 2006 Time: 7:00 PM Location: Bell 242 (UB North Campus) See you next Tuesday! -Dan >>> "DANIEL MAGNUSZEWSKI" 06/14/06 2:35 PM >>> Mongers, I have some good news! Randal Schwartz will be in town next week and he is willing to give a talk at this month's meeting (June 20th). He has two talks for us to choose from: 1) Perl Best Practices (http://www.samag.com/documents/s=10086/sam0607h/a8.htm) 2) Inside Out Objects (http://www.samag.com/documents/s=9979/sam0603g/0603g.html) Please vote for the talk that you would like to see by replying to me via email - I will keep the tally. Seeing as the meeting is less than a week away, I ask that you reply ASAP! The voting will end around 5 PM on Friday, so that I can give him a heads up on the topic. The next meeting will be held at 7PM on June 20th, in Bell 242, UB North Campus. I will be updating the website shortly. Thanks! -Dan _______________________________________________ Buffalo-pm mailing list Buffalo-pm at pm.org http://mail.pm.org/mailman/listinfo/buffalo-pm From dmagnuszewski at mandtbank.com Fri Jun 16 14:03:38 2006 From: dmagnuszewski at mandtbank.com (DANIEL MAGNUSZEWSKI) Date: Fri, 16 Jun 2006 17:03:38 -0400 Subject: [Buffalo-pm] Techpodcasts.com Roundtable Featuring YAPC and Perl Message-ID: >From the YAPC::NA website: Techpodcasts.com Roundtable Featuring YAPC http://www.techpodcasts.com has dedicated two of the three 20-minute segments of their monthly roundtable to YAPC::NA and Perl. The live event will be held tomorrow, June 17th, 2006 at 1:30 PM Pacific, 4:30 Eastern. If you are interested in attending you can sign up at http://www.techpodcasts.com/special.html From dmagnuszewski at mandtbank.com Mon Jun 19 11:31:59 2006 From: dmagnuszewski at mandtbank.com (DANIEL MAGNUSZEWSKI) Date: Mon, 19 Jun 2006 14:31:59 -0400 Subject: [Buffalo-pm] Buffalo Perl Mongers June Meeting is Tomorrow! Message-ID: Topic: Randal Schwartz on "Perl Best Practices" Date: Tuesday, June 20th, 2006 Time: 7:00 PM Location: Bell 242 (UB North Campus) This talk will be beneficial to those at every skill level, so I'd encourage everyone to attend. Check out the website for details/directions: http://buffalo.pm.org See you tomorrow! -Dan From rdice at pobox.com Mon Jun 19 15:58:54 2006 From: rdice at pobox.com (Richard Dice) Date: Mon, 19 Jun 2006 18:58:54 -0400 Subject: [Buffalo-pm] Damian Conway talks in Toronto, July 3, 4 and 5! Message-ID: <44972C2E.6030201@pobox.com> Hi everyone, By random fortune (and a flurry of last minute, behind-the-scenes emails), I have something special to announce. Damian Conway will be back in Toronto again this summer... in only 2 weeks! Damian has visited Toronto in the summers of each of 2001, 2002 and 2004, and they're always high points in Perl culture in the city. His talks are highly informative and highly entertaining. (Wednesday's talk will be especially weighted to entertaining.) This summer we have 3 events planned. //////////////////////////////////////////////// What: Perl 6 Update When: Monday July 3 (Canada Day stat holiday) 1:00 - 5:00 pm Where: 2 Bloor Street West (CIBC Tower, our usual TPM meeting spot), which is at the corner of Yonge & Bloor in downtown Toronto Room # and Floor # as yet to be determined. More details later. Note that building access could be tightly controlled, as will elevator access, so we'll have to work according to a system of pre-planned pick-up times as well as phone calls up via cellphone to get the ferryman to pick you up. Other: Dinner & beer follows, 5:30 pm - ?? Location: as yet unknown... we'll just pick a place in the neighbourhood to go following the talk. //////////////////////////////////////////////// What: Toronto BarCamp DemoCamp Damian will give a 15 minute demonstration of the Perl 6 language (That's right -- Perl 6, now!) (4 other presenters each have a chunk of time there too) When: Tuesday July 4 6:30 - 8:00 pm Where: see more/full details at: http://barcamp.org/TorCampDemoCamp7 //////////////////////////////////////////////// What: "Fun With Dead Languages" http://damian.conway.org/Seminars//DeadLanguages.html When: Wednesday July 5 6:30 - 9:00 pm Where: Not yet fully determined, likely somewhere at U. of Toronto Bahen Centre... but details to follow as they are finalized. Watch in mesmerized terror as Damian hacks code in five unrelated languages (none of them Perl). Along the way, you'll also learn about modern archaeological techniques, bidirectional cross- dressing, Ancient Greeks hackers, improbable romances, the real Club Med, why programmers shouldn't frequent casinos, the language of moisture vaporators, C++ mysticism, conversational Latin, state machines on steroids, feeding the dog the old-fashioned way, the shocking truth about anime, programming without variables or subroutines, the Four Voids of the Apocalypse, Microsoft's new advertising campaign, what the Romans used instead of braces, drunken stonemasons, the ancient probabilistic wisdom of bodkins, how to kill a language with a single byte, and the price of fish. //////////////////////////////////////////////// Fundraising ----------- There are some costs associated with his trip here. (E.g. hotel, potentially a venue for Wed. night if a free one can't be secured.) I am taking up a collection to cover the costs. Any additional money raised will be given to Damian as an honorarium, in support of such an active Perl community member who has supported us so much whenever we use Perl. In fact, I aim for there to be such a surplus so that we can help Damian out while he tours North America this summer. If you can and would like to donate please email me. Please note that all of Damian's public talks are free and that he's committed to all of them, regardless of funds raised. All are encouraged to attend -- the more, the merrier! //////////////////////////////////////////////// About Damian ---------------- For those who don't know Damian, he's from Melbourne, Australian, a professor of Computer Science at Monash University who has taken a more-or-less indefinite leave of absence so that he can work on the Perl 6 effort. (He's Larry Wall's #2 man in the design of the Perl 6 language.) He's also an active contributor to Perl 5, authoring more CPAN modules than you can comfortably shake a stick at, some being ridiculous (Coy, Acme::Bleach) while others are profound (Parse::RecDescent, Regexp::Common, Text::Balanced). He's a regular speaker at Perl and other IT conferences around the world, and a crowd favourite. His Perl books: "Perl Best Practices" http://www.oreilly.com/catalog/perlbp/ "Object Oriented Perl" http://www.manning.com/conway/ ////////////////////////////////// Any questions, comments, etc. -- just email me! Cheers, Richard From rdice at pobox.com Tue Jun 20 10:45:50 2006 From: rdice at pobox.com (Richard Dice) Date: Tue, 20 Jun 2006 13:45:50 -0400 Subject: [Buffalo-pm] Damian donations -- now paypal enabled Message-ID: <4498344E.6090408@pobox.com> Hi everyone, Our esteemed Fulko Hew has set up a Paypal donation system to help out with Damian's trip to Toronto in two weeks. If Paypal is your bag and you'd like to help out please visit: http://www.hew.ca/ Cheers, Richard From dmagnuszewski at mandtbank.com Tue Jun 20 13:03:10 2006 From: dmagnuszewski at mandtbank.com (DANIEL MAGNUSZEWSKI) Date: Tue, 20 Jun 2006 16:03:10 -0400 Subject: [Buffalo-pm] REMINDER - Buffalo Perl Mongers June Meeting is TODAY! Message-ID: Just another reminder for those who forget so easily ;-) Topic: Randal Schwartz on "Perl Best Practices" Date: Tuesday, June 20th, 2006 Time: 7:00 PM Location: Bell 242 (UB North Campus) This talk will be beneficial to those at every skill level, so I'd encourage everyone to attend. Check out the website for details/directions: http://buffalo.pm.org See you later! -Dan From dmagnuszewski at mandtbank.com Tue Jun 27 08:29:29 2006 From: dmagnuszewski at mandtbank.com (DANIEL MAGNUSZEWSKI) Date: Tue, 27 Jun 2006 11:29:29 -0400 Subject: [Buffalo-pm] Fwd: YAPC video recording: first sample Message-ID: FYI --------- Daniel Magnuszewski Systems Analyst Operating Tools M & T Bank Corporation 716.639.6834 dmagnuszewski { at } mandtbank.com http://www.mandtbank.com --------------------------- M&T Bank Corporation - "Understanding What's Important" -------------- next part -------------- An embedded message was scrubbed... From: "Chris Dolan" Subject: YAPC video recording: first sample Date: Tue, 27 Jun 2006 06:24:26 -0500 Size: 1926 Url: http://mail.pm.org/pipermail/buffalo-pm/attachments/20060627/6aab392b/attachment.mht