High_throughput_sequencing June 2011

high_throughput_sequencing@lists.fas.harvard.edu

3 participants
5 discussions

by Reardon, Claire

Dear High Throughput Sequencing Users, I'm happy to announce that the core now has a Covaris S220 shearing system available. This system is ideal for shearing nucleic acid samples when preparing libraries for Illumina sequencing. For training on the Covaris system, please contact me. The training session is free and takes about a half hour. Once trained, you may shear samples at a cost of $20 per sample. Best, Claire Claire Reardon Laboratory Manager FAS Center for Systems Biology Harvard University Northwest Lab room B239.2 52 Oxford St Cambridge, MA 02138 P: 617-384-7913 F: 617-496-0051 claire(a)cgr.harvard.edu

12 years, 11 months

Qiagen consultation

by Reardon, Claire

Dear High Throughput Sequencing Users, Our local Qiagen representative contacted me because she is looking for input from researchers doing next gen sequencing from single cells. If you're doing this kind of work and are interested in meeting with the Qiagen R&D folks, please contact me. Best, Claire Reardon Laboratory Manager FAS Center for Systems Biology Harvard University Northwest Lab room B239.2 52 Oxford St Cambridge, MA 02138 P: 617-384-7913 F: 617-496-0051 claire(a)cgr.harvard.edu

12 years, 11 months

FY12 fees for Illumina sequencing

by Reardon, Claire

Dear High Throughput sequencing users, In order to recover our costs, the rates for Illumina sequencing will increase on July 1st. We will charge the current "FY11" rate for any samples that we have in-hand by June 30th. Any samples received after June 30th will be charged at the new FY12 rates, which I've listed below. Hi Seq Cost - Harvard Account Code Cost - PO Payment Per Flow Cell Per Sample Per Flow Cell Per Sample SR 50 bp $ 7,650.00 $ 1,100.00 $ 9,600.00 $ 1,400.00 SR 100 bp $ 11,350.00 $ 1,650.00 $ 14,200.00 $ 2,100.00 PE 50 bp $ 13,500.00 $ 1,950.00 $ 16,900.00 $ 2,450.00 PE 100 bp $ 18,000.00 $ 2,600.00 $ 22,500.00 $ 3,250.00 GAII Cost - Harvard Account Code Cost - PO Payment Per Flow Cell Per Sample Per Flow Cell Per Sample SR 36 bp $ 5,100.00 $ 750.00 $ 6,400.00 $ 950.00 PE 150 bp $ 18,400.00 $ 2,650.00 $ 23,000.00 $ 3,350.00 In addition, our charge for staff-run Agilent Bioanalyzer samples will increase to $25/sample ($30 if paying by PO) and self-run Agilent Bioanalyzer chips will increase to $34/chip ($43 if paying by PO). Please let me know if you have any questions or concerns. Best regards, Claire Claire Reardon Laboratory Manager FAS Center for Systems Biology Harvard University Northwest Lab room B239.2 52 Oxford St Cambridge, MA 02138 P: 617-384-7913 F: 617-496-0051 claire(a)cgr.harvard.edu

12 years, 11 months

high throughput sequencing user meeting

by Reardon, Claire

Dear Sequencing Users, Our next user group meeting will be tomorrow at 1pm in room 425. Join us to discuss version 3 kits for the HiSeq, the new Covaris shearing system, and any other issues you'd like to bring up. See you there, Claire

12 years, 12 months

FW: [Bioinformatics.Org] On-site summer course on bioinformatics programming

by Karger, Amir

Another upcoming programming course. -Amir Karger -----Original Message----- From: Bioinformatics.Org [mailto:postman@dallas0.bioinformatics.org] Sent: Monday, June 06, 2011 12:52 AM To: Karger, Amir Subject: [Bioinformatics.Org] On-site summer course on bioinformatics programming -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- CS101 Introduction to Bioinformatics Programming July 28-29, 2011 *ON-SITE* in Cambridge, Massachusetts, USA -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- ***This is a special offering of our introductory programming course, given in-person in Kendall Square, Cambridge, Massachusetts.*** OBJECTIVES: This course teaches IT specialists, entry level bioinformaticians and biologists to leverage Linux and various open-source bioinformatics tools, together with scripting and data management tools, to perform computations in biological research and create information from data. Examples in this course will use data from DNA and amino acid sequences, microarray profiles, images, mass spectrometry, LIMS, and biological annotations. SYLLABUS: The course is divided into 4 sessions, with roughly 1-1.5 hours of lecture, and additional time for lab exercises. A 5th session is reserved for project discussion and any other course relevant issues the students may want to discuss. Session 1 will cover an overview of the computing landscape for bioinformatics. Common data management and mining issues will be highlighted, alongwith an overview of challenging problems and their solutions. Linux OS overview will be done, alongwith lab exercises to get participants familiar with Linux. Session 2 will cover fundamentals of scripting with Perl, such as scalars, arrays, variable interpolation, operators (mathematics, conditional, logical), file input/output, printing, loops (if-then-else, for, while), list operations, etc. Lab exercises will be conducted Session 3 will cover functions/ subroutines, hash arrays and regular expressions. Participants will be introduced to MySQL databases. Session 4 will cover the installation of Perl packages, and some examples of using the famous package BioPerl for manipulating sequences, automating BLAST queries, etc. Project will be assigned that uses BioPerl and the Perl Database interface PREREQUISITES: No programming experience is required, just a need to learn how to program. FOR MORE INFORMATION: For tuition costs and other inquiries, please contact edu(a)bioinformatics.org. ---------------------------------------- This message is being sent to you because you chose to receive notices about new offerings at Bioinformatics.Org. To change this, please log into your account and uncheck the relevant box on this webpage: http://www.bioinformatics.org/account/ Sent to: akarger(a)cgr.harvard.edu

12 years, 12 months

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High_throughput_sequencing June 2011