Dear Colleagues,
We hope that you are doing well in 2011, and are excited to update you about IDAWG projects and plans for this year.
New IDAWG web domain: immunogenomics.org
We have registered a new, and hopefully easier to recall, domain name for the IDAWG web pages -- immunogenomics.org.
We will retain the original igdawg.org domain name, but we hope that immunogenomics.org will make it easier to find the IDAWG site. Please let us know if you encounter any problems using the immunogenomics.org address.
Software updates and new web tools
At the end of last year, we released an update to the Allele Name Translation Tool software (ANTT version 0.5.0), which includes software improvements and new settings for the control of the information written to the log files.
This distribution of the ANTT also includes two new sets of translation tables. One set, developed by Pierre-Antoine, will expand the so-called "g-codes" for nomenclature version 2 allele names that share the identical antigen recognition sequence to strings of slash-delimited version 2 allele names (e.g. A*0101g will be translated to A*01010101/01010102N/0104N/0122N/0132/0134N/0137).
A second set includes complete allele name truncations (e.g. in addition to A*01010101 and A*01:01:01:01, these tables also include A*01, A*0101, A*010101, and A*01, A*01:01, and A*01:01:01), and increases the speed of translation for dataset that include large numbers of right-truncated allele-names. Visit immunogenomics.org/software.html to find these updates.
We are releasing beta-versions of two new web-based immunogenomics tools, iHAP Beta, and the GFM Browser. Please take a look and let us know what you think. The iHAP Beta tool uses an implementation of an E-M algorithm available in the R Haplo Stats package to perform multi-locus haplotype estimation over the internet. The Global Frequency Map (GFM) Browser allows side-by-side comparison and browsing of the HLA allele frequency maps available at www.pypop.org/popdata. We hope to expand the functionality of both IHAP Beta and the GFM Browser over the course of the year, and welcome your input.
IDAWG Commentary for Tissue Antigens
We submitted the commentary manuscript to Tissue Antigens at the end of last year, and received helpful comments from two reviewers in February.
We think that most of the reviewers' comments can be addressed easily. Please let us know your thoughts about the reviewers' comments and any suggestions for improvements to the manuscript;
we would like to discuss a revised manuscript and a draft response to the reviewers at the EFI meeting next month.
The Nature Genetics editorial mentioned by Reviewer #2 can be found at: http://www.nature.com/ng/journal/v42/n11/full/ng1110-915.html.
2010 ASHI Conference Minutes
The minutes from the IDAWG meeting at the 2010 ASHI conference are available online. Please review them and let us know if any modifications are necessary.
IDAWG 16th IHI Workshop Project
At last year's ASHI meeting, we discussed the development of a survey of immunogenetic community data-management and analysis practices.
ASHI is generously giving us the support to make the survey available over the internet via the SurveyMonkey web site before the EFI meeting.
We aim to present the data collected and inferences derived from the survey at the 16th IHIW meeting.
In addition, the overview of community data-management and analysis practices provided by the survey will inform the specifics of the STREIS statement.
Please review the draft survey questions. We hope that you will all be interested in participating in the survey; please let us know if you are interested, as well as any thoughts that you may have about the survey questions.
2011 EFI Conference
The 2011 EFI meeting will be held in next month in Prague, Czech Republic from May 4-7. The IDAWG will meet during the conference on May 4th from 1500 to 1700 in Meeting room III on the 2nd floor, and we hope that you will be able to attend.
We will have internet access in the meeting room, so any of you who cannot attend in person will either be able to connect to the meeting via Skype, or we can make a Skype call to specific phone numbers for those of you who cannot use Skype.
Please let us know if you will be able to attend the meeting (either in person or via Skype), or if you would like us to call you.
Please let us know if there are any items you would like to put on the agenda for this meeting. Currently we would like to discuss the revision to the commentary, the 16th Workshop project, and development of a formal relationship between the IDAWG and EFI along the lines of our relationships with ASHI, via the Scientific and Clinical Affairs Committee, and APHIA, via the QAP and Standardisation Subcommittee.
Finally, the abstract we submitted describing the 16th IHIW survey (IDAWG 16th IHIWS Project: Immunogenomic Data Management Methods) will be presented as a poster on Thursday May 5 from 1700-1830 at the Wine & Cheese reception on Terrace I and II. We plan to have PDF copies of the survey available for EFI attendees to complete, as well as a laptop connected to the SurveyMonkey site if there is internet access in the poster area. Please let us know if you will be attending the EFI conference, and be sure to stop by the poster.
Funding Update
If you recall, we submitted a revision of our NIH R01 proposal seeking funding to support the efforts of the working group in July of 2010.
Unfortunately, that proposal will not be funded, but we continue to look for opportunities to obtain support for the efforts of the working group.
We are looking forward to working with you on our many projects in 2011.
Cheers,
Steve and Jill