From clements from nescent.org Wed Apr 9 16:27:24 2008 From: clements from nescent.org (Dave Clements) Date: Wed Apr 9 16:32:20 2008 Subject: [Molecular-evolution] GMOD Summer School, Application Deadline April 15 Message-ID: Hello, This is a reminder that we will start reviewing applications for the GMOD Summer School one week from today, on Wednesday, April 15. If you are interested in attending then please submit a statement of interest by the end of April 15. See http://gmod.org/GMOD_Summer_School and http://gmod.org/GMOD_Summer_School_Statement_of_Interest for more information. Please let me know if you have any questions. Thanks, Dave Clements GMOD Help Desk On Mon, Mar 24, 2008 at 1:32 PM, Dave Clements wrote: > GMOD Summer School > 11-13 July, 2008 > National Evolutionary Synthesis Center (NESCent) > Durham, North Carolina, USA > > The first GMOD Summer School (http://gmod.org/GMOD_Summer_School) will > be held July 11-13, 2008 at the National Evolutionary Synthesis Center > (NESCent), in Durham, North Carolina, USA. GMOD is a collection of > interoperable open source software components for managing genomic > data. GMOD components are used in diverse contexts, with both > emerging and established model organisms. > > The course will provide an overview of GMOD and cover these popular > components in detail: > * Chado - a modular and extensible database schema > * Apollo - genome annotation editor > * GBrowse - genome viewer > * CMap - comparative map viewer > * Community Annotation System - GMOD's most popular components in a > single system > > This is a 2 1/2 day hands-on workshop aimed at teaching new GMOD users > how to get up and running with popular GMOD components. There will > also be a concurrent 1 day session aimed at principal investigators > that will give decision makers an overview of what GMOD can do, how > the project operates, and what level of resources are needed to use > GMOD. > > The National Evolutionary Synthesis Center (NESCent, > http://nescent.org) has joined the GMOD project with the goal of > lowering the barrier to entry for research communities focused on > emerging model organisms. The GMOD Summer School is a part of this > effort. NESCent is also extending GMOD components, particularly > Chado, to better support comparative and evolutionary data. > > If you are interested in attending the GMOD Summer School please > submit a Statement of Interest before April 15, 2008. The course is > free but enrollment is limited. For application information and a > tentative program see: > > http://gmod.org/GMOD_Summer_School > > Please let me know if you have any questions, comments, or requests. > > Thanks, > > Dave Clements > GMOD Help Desk > help@gmod.org > ------------------------ > NESCent offers various courses and workshops, as well as funding > post-doctoral and sabbatical positions, working groups and other > meetings. For more information about research and training > opportunities at NESCent, visit our website at www.nescent.org. Sign > up for our quarterly electronic newsletter at > http://www.nescent.org/about/contact.php to automatically receive > information about events at NESCent. > From stevet from bio.fsu.edu Wed Apr 23 12:41:04 2008 From: stevet from bio.fsu.edu (Steve Thompson) Date: Wed Apr 23 13:23:47 2008 Subject: [Molecular-evolution] Other: Accelrys petition followup Message-ID: <20080423114117.X29516@epsilon.bio.fsu.edu> Hi all - re. http://www.petitiononline.com/gcg/ A huge THANKS to all of you that signed my petition! Within the first week online I got almost 150 signatures, and John Devereux himself most recently signed it. I sent Rob Brown of Accelrys an 'official' copy of the petition and the signatures at the end of last month. However, but not surprisingly, I have yet to receive one word back from Accelrys. I realize that we can't force them to do anything, but I at least thought that they would have the courtesy to respond to it somehow. The petition did result in a news story though. GenomeWeb News' bioinformatics newsletter, BioInform, published the story on April 4th. See my copy at: http://bio.fsu.edu/~stevet/BioInformGCG.pdf Some may feel that the BioInform story suggests the petition was merely a means of influencing commercial negotiations with Accelrys regarding code release, and have nothing to do with public domain availability, but this was never my objective. It is and remains a plea not to kill the package, and in particular SeqLab, by whatever means possible, but preferably within some type of open source arrangement. Furthermore, Accelrys argues in the article that many more people have signed the petition than subscribe to the package, and that this somehow invalidates the petition. This is completely irrelevant as the GCG license has always been to an institution, allowing as many people in that institution access as wanted, not to individual investigators. Here at FSU I have supported over 100 GCG users with one GCG license over the years. June should be interesting for us all. We'll have to see if Accelrys honors their commitment to those of us with "perpetual" licenses to provide non-node-locked, non- expiring versions of the license after June 30, 2008. Time will tell. Cheers - Steve Steven M. Thompson A C T G stevet@bio.fsu.edu \-/ http://bio.fsu.edu/~stevet/cv.html /\ /--| FSU SCS / BioInfo 4U /---/ |--/ Florida State University School of \-/ Computational Science /\ /--\ 1st floor DIRAC 150G |---\ Tallahassee, Florida \---\ 32306-4120 \--| 850-644-4490 \-/ /\ 2538 Winnwood Circle /--\ Valdosta, Georgia /---| 31601-7953 |--/ 229-249-9751 From stevet from bio.fsu.edu Fri Apr 25 08:16:28 2008 From: stevet from bio.fsu.edu (Steve Thompson) Date: Fri Apr 25 08:56:28 2008 Subject: [Molecular-evolution] Other: followup to Accelrys petition followup Message-ID: <20080425085739.N36764@epsilon.bio.fsu.edu> Hello all - A brief note to let you know what's happened since my posting this last Wednesday: Rob Brown of Accelrys did contact me, finally. He says, and I quote: "The petition and the subsequent BioInform article produced a significant response and generated inquiries from a number of third party companies who now wish to discuss various possibilities relating to GCG with us. We are now in the process of following up on all of those which is taking some time." So, it looks like some good has come out of the process, although this doesn't look like the open source type of arrangement that many of us hoped for. Regardless, it may mean that the package will not be dying. And, Accelrys sent me my new non-node-locked, non-expiring license key! Cheers - Steve Steven M. Thompson A C T G stevet@bio.fsu.edu \-/ http://bio.fsu.edu/~stevet/cv.html /\ /--| FSU SCS / BioInfo 4U /---/ |--/ Florida State University School of \-/ Computational Science /\ /--\ 1st floor DIRAC 150G |---\ Tallahassee, Florida \---\ 32306-4120 \--| 850-644-4490 \-/ /\ 2538 Winnwood Circle /--\ Valdosta, Georgia /---| 31601-7953 |--/ 229-249-9751 From stevet from bio.fsu.edu Sun Apr 27 19:08:49 2008 From: stevet from bio.fsu.edu (Steve Thompson) Date: Sun Apr 27 19:46:35 2008 Subject: [Molecular-evolution] Other: another followup (apology) Message-ID: <20080427200719.B51990@epsilon.bio.fsu.edu> Hi all - I would like to offer my apology to Accelrys and its employees for suggesting that the company would not follow through on their commitment to supply non-node-locked, non-expiring license keys to all current GCG custyomers with "perpetual" licenses. As I mentioned in my last posting Accelrys is now involved in that process and I have received my new key. It was never my intent to discredit Accelrys, nor its employess. I merely had not been informed that the process was underway. I am sorry that I miswrote and hope that any hard feelings can be overcome. Thank you. Cheers - Steve Steven M. Thompson A C T G stevet@bio.fsu.edu \-/ http://bio.fsu.edu/~stevet/cv.html /\ /--| FSU SCS / BioInfo 4U /---/ |--/ Florida State University School of \-/ Computational Science /\ /--\ 1st floor DIRAC 150G |---\ Tallahassee, Florida \---\ 32306-4120 \--| 850-644-4490 \-/ /\ 2538 Winnwood Circle /--\ Valdosta, Georgia /---| 31601-7953 |--/ 229-249-9751