From eleanora at jimmy.harvard.edu Tue Jun 9 14:25:10 2009 From: eleanora at jimmy.harvard.edu (Eleanor Howe) Date: Tue, 09 Jun 2009 16:25:10 -0400 Subject: [TM4-Announce] Request for letters of Support for the MeV Renewal application Message-ID: <4A2EC526.1010108@jimmy.harvard.edu> Friends, As many of you may know, the development of MeV has been supported by a grant from the National Library of Medicine of the US National Institutes of Health. This modest level of funding has allowed us to support development of MeV through the addition of features and to provide support to users who identify potential problems with the software or who have specific needs for additions or extensions. I hope that over the years MeV has been a useful tool supporting both your research and your educational work and that you have found MeV to something of value. Our funding for MeV is slated to end in 2010 and so I am now preparing a renewal application to request continued support for the MeV project. The MeV team and I have been discussing what we would want to add as part of our renewal proposal. We plan to continue adding features for the analysis of array-based data, to provide support for integrated analysis of multiple data types from the same sample (mRNA and miRNA; mRNA expression and methylation; expression and CNV data, expression and SNP profiles, for example), to provide better integration with genomic resources (such as genome browsers), and to better integrate with analytical tools from the BioConductor project and with utilities such as Cytoscape. More importantly for many of you, we will propose to expand our capabilities to sequence-based methods such as Digital Gene Expression, RNA-Seq, and ChIP-Seq, to name a few examples. And of course, we plan to continue to make MeV freely available as an open-source project. To do this, we need to demonstrate some tangible level of community support for the project - beyond the more than 20,000 downloads in the past year and the 821 citations of the initial paper describing the software. And the most important way we can do that is through getting letters of support from the community. If you are able to support our project, I would greatly appreciate it if you would send a brief letter (as a PDF) describing how MeV has helped you in your research or teaching and expressing your enthusiasm for continued funding. To make this easy, I have taken the liberty of drafting a letter that you can modify as you see fit. The draft can be found at http://www.tm4.org/mev/request_for_letters.html. Please send copies of your letters as PDFs directly to me at johnq at jimmy.harvard.edu. And thank you for your support! John Quackenbush From tm4-announce at tm4.org Wed Jun 10 19:13:41 2009 From: tm4-announce at tm4.org (Announcements for the TM4 Microarray Software Suite (http://www.tm4.org/)) Date: Wed, 10 Jun 2009 21:13:41 -0400 Subject: [TM4-Announce] Letters of support Message-ID: <4A305A45.502@jimmy.harvard.edu> My friends, One request, if possible. Could you put the letters on letterhead and send the PDF? Thank you all for your support. John Quackenbush From tm4-announce at tm4.org Mon Jun 22 10:42:05 2009 From: tm4-announce at tm4.org (Announcements for the TM4 Microarray Software Suite (http://www.tm4.org/)) Date: Mon, 22 Jun 2009 12:42:05 -0400 Subject: [TM4-Announce] Request for letters of support Message-ID: <4A3FB45D.5010301@jimmy.harvard.edu> Friends, Just a reminder and a request. The grant that supports MeV is up for renewal. One of the things that helped us in our application for funding four years ago was a list of more than 100 supporting letters. We currently have slightly more than 50 and need to get another 50 before early next week if we are going to be able to include this in the application. I've included a draft letter below which you can modify (and I encourage you to do this) to reflect how you use MeV and the impact it has had on your research or teaching. If you could send me a copy (mailto:johnq at jimmy.harvard.edu) as a PDF on your institutional letterhead, I would appreciate it immensely. Thank you in advance for your help. JQ John Quackenbush Dana-Farber Cancer Institute 44 Binney Street, Sm822 Boston, MA 02115 [DATE] Dear Dr. Quackenbush, I want to begin by thanking you and your team for supplying the research community with MeV. This software is outstanding, providing professional quality research tools in a user-friendly package at absolutely no cost and with no restrictions on its use. MeV has been extremely important in our research and has allowed us to [EXAMPLE]. Further, MeV has become an important part of our educational mission. I use it regularly in teaching the basics of microarray analysis to my students. It is easy to use, easy to learn, and the documentation and example datasets you provide are outstanding starting points for our students to learn about genomic methods and their applications. I understand that your existing funding to support development of MeV is scheduled to end in 2010 and that you are currently preparing a renewal application to continue funding into the future. Your plans to extend MeV to deal more effectively with large datasets, to better accommodate SNP, CNV, and ChIP, and other new data types, and to deal with sequence-based genomic assays ranging from Digital Gene Expression and RNA-Seq to ChIP-Seq and beyond are the types of additions that I too believe are essential for future biomedical research. The combination of these proposed additions with MeV?s intuitive interface, the new displays you are proposing to incorporate, integration with other tools such as Cytoscape and the BioConductor utilities, and outstanding data integration methods you are building will guarantee that MeV is an essential research tool and an asset to a wide range of planned and ongoing research projects. As a member of the large (and still growing) community of MeV users, I fully support your application and I hope that the NIH sees the value in continuing so support this important research resource. Best of luck with your application. Sincerely, [Your name and titles]