JANUARY 9, 2013
Happy new years to everyone. A couple new things happening in BioMicro that we want to make everyone aware of.
First, this month begins a year long experiment in joining the BioMicro Center Informatics team and the KI Bioinformatics and Computing Core in to a single team. Our two teams have been collaborating for several years, sharing computational infrastructure, etc. but this year we will be formalizing and expanding the relationship with the goal of creating a more efficient unified core. Informatics analysis requests should still be sent to Charlie Whittaker or to myself as usual, but will be spread across the joint team based on expertise and on availability. You are also, as always, welcome to contact any of the informatics scientists directly. We hope this will allow us to reduce waiting times and to keep costs under control.
During the trial period (and hopefully going forward), pricing for informatics will be available in two flavors. First, for projects needing routine work, the subsidized rate will be $70/h for all CORE members (Biology, BE, KI, CEHS). For more involved projects, we have second option to purchase a “share” of the informatics team. This is an annual commitment for a fraction of an informaticist and will cost $960/mo for an average of 4h/week of informatics support. The monthly usage levels do not have to be exact and can be used in large blocks. The hours in the share can be used with any member of the team and the informaticist can vary from project to project.
Finally, and importantly, we will be changing the way we are storing Illumina sequencing data long term. In the past, we have saved the fastq, sam and bam files, along with the quality control data, in a zipped file. These zipped files now occupy over 50TB of storage which is limiting how we are able to handle new sequencing runs. To address this, we will be deleting the fastq and sam files from the archive and storing only the binary bam and quality control files. The fastq and sam files can be regenerated rapidly from the bam files using Picard and SamTools (though reads may not be in the same order). As always, we strongly encourage you to keep your own copy of the Illumina data and use our version only as a backup. We will begin this conversion next week.
If you have any concerns, please do not hesitate to contact me.
- Wamstad JA, Alexander JM, Truty RM, Shrikumar A, Li F, Eilertson KE, Ding H, Wylie JN, Pico AR, Capra JA, Erwin G, Kattman SJ, Keller GM, Srivastava D, Levine SS, Pollard KS, Holloway AK, Boyer LA, and Bruneau BG. . pmid:22981692.
- Minot S, Melo MB, Li F, Lu D, Niedelman W, Levine SS, and Saeij JP. . pmid:22847430.
- Kelly L, Huang KH, Ding H, and Chisholm SW. . pmid:22102570.
- Mellios N, Sugihara H, Castro J, Banerjee A, Le C, Kumar A, Crawford B, Strathmann J, Tropea D, Levine SS, Edbauer D, and Sur M. . pmid:21892155.
- Kagey MH, Newman JJ, Bilodeau S, Zhan Y, Orlando DA, van Berkum NL, Ebmeier CC, Goossens J, Rahl PB, Levine SS, Taatjes DJ, Dekker J, and Young RA. . pmid:20720539.
- Dejosez M, Levine SS, Frampton GM, Whyte WA, Stratton SA, Barton MC, Gunaratne PH, Young RA, and Zwaka TP. . pmid:20581084.
- Boselli M, Rock J, Unal E, Levine SS, and Amon A. . pmid:19531355.
RECENT CHANGES TO THE WEBSITE
30 July 2015