From csbi-events at mit.edu Thu Dec 1 11:36:09 2005 From: csbi-events at mit.edu (csbi-events@mit.edu) Date: Thu, 1 Dec 2005 11:36:09 -0500 Subject: [CSBi-events] Upcoming Seminar Message-ID: Dear CSBi Members, FYI Machine Visual Screening MIT Machine Vision Seminar 2005/2006 Speaker: Arman M. Garakani Speaker Affiliation: Reify corporation Host: Berthold K.P. Horn Host Affiliation: MIT CSAIL Date: 12-14-2005 Time: 2:45 PM - 3:45 PM Location: Patil/Kiva Seminar Room (32-G449) Biologists have always relied on viewing biological systems as they evolve in space and time. Most of us -- even non biologists -- can recognize a dynamic biological event such as a beating heart, a dividing, migrating or spreading cell. How is it that we can "label" these events without imposing a model? One explanation may be that the entire event projects information about its dynamic nature. Oscillating events may be recognized by their repetitive presentation. Similarly, spreading events may be recognized by their continuously enlarging presentation. A visual event is captured digitally into a snapshot sequence. Measuring similarity between any snapshot and all other snapshots is particularly hard. The transformation between two snapshots has to describe geometric changes of deformable objects, illumination changes, intensity changes, and so on. If there were no mutual information in a visual event, it would be impossible to measure similarity among its snapshots. In our experience, most biological events, when captured appropriately, are consistent and contain measurable mutual information. During this talk, I will describe our work at Reify corporation. We have developed a set of technologies to extract and measure biological events enabling "machine visual screening" of biology. We measure the mutual information inherent in an image sequence digital capture of a biological event. We call this measurement the Aggregate Change Index (ACI). ACI can in many cases be directly used as a functional readout. In many other cases it can form a robust basis of other functional readouts. Whether measuring mechanical work of motor proteins or heart function of a young zebra fish for a phenotypic compound profiling, ACI and other mutual information based measurements present the possibility of unbiased, robust, and repeatable functional readouts of the marvellously consistent set of systems that is Biology. ------------------------------------ Bio: ------------------------------------ Arman Garakani is co-founder and chief technology officer at Reify corp. He was previously at Cognex corp where he played an instrumental part in vision software and algorithm development. Arman's graduate research was in computational methods in Fluid Mechanics at Alden Laboratory; one of the oldest continuously operating hydraulic laboratories in the world. Arman holds a BS in Mechanical Engineering from Worcester Polytechnic Institute and an MS in Management of Technology from MIT. -- Linda K. Earle, Outreach Coordinator Computational and Systems Biology (CSBi) Phone: (617) 324-0074 Fax: (617) 324-0081 Massachusetts Institute of Technology 77 Massachusetts Avenue Building 68 - Room 459 Cambridge, MA 02139 From csbi-events at mit.edu Mon Dec 5 11:57:28 2005 From: csbi-events at mit.edu (csbi-events@mit.edu) Date: Mon, 5 Dec 2005 11:57:28 -0500 Subject: [CSBi-events] CSBi Seminar - Dr. Ben Blencowe - 12/9 Message-ID: Dear CSBi Community, You may want to take note of the upcoming CSBi Speaker Series seminar on Friday, December 9. Please join us if your schedule permits. Thanks very much. -------------------------------------------------------------------------------- Dr. Benjamin J. Blencowe Banting and Best Department of Medical Research and Center for Cellular and Biomolecular Research University of Toronto Global Analysis of Mammalian Alternative Splicing using a Quantitative Microarray Platform Friday, December 9, 2005 Maclaurin Building (4-270) 3:00 - 4:00 p.m. Light refreshments served. Abstract Alternative splicing (AS), the process by which exons in primary transcripts are joined in different combinations to generate multiple mRNA variants, represents an important mechanism for the expression of structurally and functionally distinct proteins from a limited number of genes. A major goal of the postgenomic era is to define physiologically- and disease-relevant AS events, in particular, where and when these events occur, what their specific roles are, and how they are integrated and regulated in the context of global gene expression patterns. To address these questions, we have developed a quantitative microarray platform for the global analysis of AS1. Profiling of "cassette-type" alternative exons in diverse mouse tissues has resulted in the identification of thousands of new tissue-specific AS events, insights into how the evolutionary origin of exons influences their global inclusion levels, and information on how transcription and AS are coordinated globally to define tissue type. More recently, we have used the microarray platform to investigate the global exon targets of specific splicing factors and the role of AS in the regulation of gene expression via the process of nonsense-mediated mRNA decay. In addition, we are employing new microarray designs and profiling data to identify and characterize factors associated with cell and tissue type-specific regulation of AS. Progress in these areas will be presented. 1 Pan et al. (2004) Mol Cell 16: 929-941 Host: Dr. Christopher B. Burge Biology Department and Biological Engineering Contact: Brenda E. Pepe 617.452.3885 http://csbi.mit.edu/ Sponsored by CSBi Annual CSBi Seminar Series in Computational and Systems Biology The entire MIT Community is welcome to attend! -- From csbi-events at mit.edu Wed Dec 7 13:23:34 2005 From: csbi-events at mit.edu (csbi-events@mit.edu) Date: Wed, 7 Dec 2005 13:23:34 -0500 Subject: [CSBi-events] (Reminder) CSBi Seminar-Dr. Ben Blencowe 12/9 Message-ID: Dear CSBi Community, This note is simply a reminder of our upcoming CSBi Speaker Series seminar on Friday, December 9. Please join us if your schedule permits. Thanks very much. -------------------------------------------------------------------------------- Dr. Benjamin J. Blencowe Banting and Best Department of Medical Research and Center for Cellular and Biomolecular Research University of Toronto Global Analysis of Mammalian Alternative Splicing using a Quantitative Microarray Platform Friday, December 9, 2005 Maclaurin Building (4-270) 3:00 - 4:00 p.m. Light refreshments served. Abstract Alternative splicing (AS), the process by which exons in primary transcripts are joined in different combinations to generate multiple mRNA variants, represents an important mechanism for the expression of structurally and functionally distinct proteins from a limited number of genes. A major goal of the postgenomic era is to define physiologically- and disease-relevant AS events, in particular, where and when these events occur, what their specific roles are, and how they are integrated and regulated in the context of global gene expression patterns. To address these questions, we have developed a quantitative microarray platform for the global analysis of AS1. Profiling of "cassette-type" alternative exons in diverse mouse tissues has resulted in the identification of thousands of new tissue-specific AS events, insights into how the evolutionary origin of exons influences their global inclusion levels, and information on how transcription and AS are coordinated globally to define tissue type. More recently, we have used the microarray platform to investigate the global exon targets of specific splicing factors and the role of AS in the regulation of gene expression via the process of nonsense-mediated mRNA decay. In addition, we are employing new microarray designs and profiling data to identify and characterize factors associated with cell and tissue type-specific regulation of AS. Progress in these areas will be presented. 1 Pan et al. (2004) Mol Cell 16: 929-941 Host: Dr. Christopher B. Burge Biology Department and Biological Engineering Contact: Brenda E. Pepe 617.452.3885 http://csbi.mit.edu/ Sponsored by CSBi Annual CSBi Seminar Series in Computational and Systems Biology The entire MIT Community is welcome to attend! -- From csbi-events at mit.edu Thu Dec 8 10:04:02 2005 From: csbi-events at mit.edu (csbi-events@mit.edu) Date: Thu, 8 Dec 2005 10:04:02 -0500 Subject: [CSBi-events] 2006 CSBi Symposium - Register Now Message-ID: Systems Biology of Stem Cells 2006 CSBi Symposium January 12, 2006 Kresge Auditorium, MIT Please join us for the CSBi Symposium, January 12, 2006 on the Systems Biology of Stem Cells. Started in 2003, the annual CSBi symposium has brought together participants interested in systems biology from around the country. The 2006 Symposium features prominent speakers from MIT and other academic institutions in the US and abroad who will address critical problems at the interface of stem cells and systems biology. REGISTER BEFORE DECEMBER 31, 2005 at http://csbi.mit.edu/events/annualsymposium/2006/registration Program 7:30 am Registration and Coffee 8:15 am Welcome Remarks Paul Matsudaira CSBi, Whitehead Institute for Biomedical Research, and MIT Session One 8:20 am Chair Rudolf Jaenisch Whitehead Institute for Biomedical Research and MIT 8:30 am Ihor Lemischka Princeton University Exploring Cell Fate Regulation in Stem Cells 9:15 am David Gifford MIT Embryonic Stem Cell Regulatory Networks 10:00 am Break 10:30 am Elaine Fuchs Howard Hughes Medical Institute and The Rockefeller University Stem Cells of the Skin and their Lineages 11:15 am Allan Spradling The Carnegie Institution of Washington The Anatomical Genomics of Drosophila Stem Cells 12:00 pm LUNCH-Salon de Puerto Rico, MIT Student Center Session Two 1:35 pm Chair Doug Lauffenburger CSBi and MIT 1:45 pm Alejandro S?nchez-Alvarado Howard Hughes Medical Institute and University of Utah, School of Medicine Schmidtea mediterranea: Regeneration as a Cell Population Dynamics Problem 2:30 pm Stanislav Shvartsman Lewis-Sigler Institute for Integrative Genomics and Princeton University Cell Fate Determination in Developing Tissues 3:15 pm Break 3:45 pm Lucy Shapiro Stanford University, School of Medicine Architecture of the Regulatory Circuit that Coordinates the Modular Organization of the Cell Cycle 4:30 pm Eric Davidson California Institute of Technology A Developmental Control System: The Sea Urchin Embryo Gene Regulatory Network 5:15 pm Closing Remarks Bruce Tidor CSBi and MIT From csbi-events at mit.edu Wed Dec 14 11:44:27 2005 From: csbi-events at mit.edu (csbi-events@mit.edu) Date: Wed, 14 Dec 2005 11:44:27 -0500 Subject: [CSBi-events] Seminar next week of interest Message-ID: Dear CSBi members, this may be of interest to you: CSBi - Community Computing Resources Meetings "CSAIL Network and Computing Infrastructure" Jonathan D. Proulx, Senior Systems Administrator CSAIL Tuesday, December 20 12-1 Stata Center - Star Room 32-D463 -- Linda K. Earle, Outreach Coordinator Computational and Systems Biology (CSBi) Phone: (617) 324-0074 Fax: (617) 324-0081 Massachusetts Institute of Technology 77 Massachusetts Avenue Building 68 - Room 459 Cambridge, MA 02139 From csbi-events at mit.edu Thu Dec 15 15:03:51 2005 From: csbi-events at mit.edu (csbi-events@mit.edu) Date: Thu, 15 Dec 2005 15:03:51 -0500 Subject: [CSBi-events] CSBi Seminar Series - SAVE THE DATE! Message-ID: Dear CSBi Community, Please take note of our Spring 2006 seminar series events and plan to join us if your schedule permits. Further details to follow in the weeks ahead. Please check the CSBi website too! Friday, February 10, 2006 Dr. Adam Arkin University of California, Berkeley Host: Dr. Andrew Endy Friday, March 3, 2006 Dr. Andrew Endy Massachusetts Institute of Technology Host: Dr. Douglas Lauffenburger Friday, April 21, 2006 Dr. Carlos Bustamante University of California, Berkeley Host: Dr. Robert T. Sauer Friday, April 28, 2006 Dr. Timothy Hughes University of Toronto Host: Dr. Christopher B. Burge Thanks! -- From csbi-events at mit.edu Mon Dec 19 08:14:44 2005 From: csbi-events at mit.edu (CSBi events notifies members of all upcoming events.) Date: Mon, 19 Dec 2005 08:14:44 -0500 Subject: [CSBi-events] REMINDER CSBi SEMINAR TUESDAY THE 20TH Message-ID: Dear CSBi members, this may be of interest to you: CSBi - Community Computing Resources Meetings "CSAIL Network and Computing Infrastructure" Jonathan D. Proulx, Senior Systems Administrator CSAIL Tuesday, December 20 12-1 Stata Center - Star Room 32-D463 Jonathan D. Proulx, Senior Systems Administrator CSAIL, will describe the "CSAIL Network and Computing Infrastructure" as part of the CSBi Computing Resources series. The purpose of the computing series is to alert CSBi members of the capabilities of the computing resources that are associated with CSBi. In the past two talks, Jay Copeland and Al Davis, described how processors and storage in BioMicro and the WI-MIT BioImaging Center are networked with various instruments and support high end computing problems. Please join us in learning about the capabilities of the CSAIL domain. -- Linda K. Earle, Outreach Coordinator Computational and Systems Biology (CSBi) Phone: (617) 324-0074 Fax: (617) 324-0081 Massachusetts Institute of Technology 77 Massachusetts Avenue Building 68 - Room 459 Cambridge, MA 02139 From csbi-events at mit.edu Fri Dec 16 09:29:13 2005 From: csbi-events at mit.edu (CSBi events notifies members of all upcoming events.) Date: Fri, 16 Dec 2005 09:29:13 -0500 Subject: [CSBi-events] CSBi Seminar Series - SAVE THE DATE! In-Reply-To: References: Message-ID: Hi - Just to let you know, Dr. Endy goes by Drew. ;) Sincerely, JoAnn >Dear CSBi Community, > >Please take note of our Spring 2006 seminar series events and plan >to join us if your schedule permits. Further details to follow in >the weeks ahead. Please check the CSBi website too! > >Friday, February 10, 2006 >Dr. Adam Arkin >University of California, Berkeley >Host: Dr. Andrew Endy > >Friday, March 3, 2006 >Dr. Andrew Endy >Massachusetts Institute of Technology >Host: Dr. Douglas Lauffenburger > >Friday, April 21, 2006 >Dr. Carlos Bustamante >University of California, Berkeley >Host: Dr. Robert T. Sauer > >Friday, April 28, 2006 >Dr. Timothy Hughes >University of Toronto >Host: Dr. Christopher B. Burge > >Thanks! >-- >_______________________________________________ >CSBi-events mailing list >CSBi-events at mit.edu >http://mailman.mit.edu/mailman/listinfo/csbi-events -- JoAnn B. Sorrento Senior Administrative Assistant to Professor Douglas A. Lauffenburger, Director, Biological Engineering Division Rm. 56-341, 77 Massachusetts Avenue Cambridge, MA 02139 617-253-7420 (O); 617-258-0204 (F) From csbi-events at mit.edu Thu Dec 29 14:49:03 2005 From: csbi-events at mit.edu (CSBi events notifies members of all upcoming events.) Date: Thu, 29 Dec 2005 14:49:03 -0500 Subject: [CSBi-events] 2006 CSBi Symposium - Deadline Dec 31, 2005 Message-ID: Just a Reminder: Registration deadline is December 31, 2005 Systems Biology of Stem Cells 2006 CSBi Symposium January 12, 2006 Kresge Auditorium, MIT Please join us for the CSBi Symposium, January 12, 2006 on the Systems Biology of Stem Cells. Started in 2003, the annual CSBi symposium has brought together participants interested in systems biology from around the country. The 2006 Symposium features prominent speakers from MIT and other academic institutions in the US and abroad who will address critical problems at the interface of stem cells and systems biology. REGISTER BEFORE DECEMBER 31, 2005 at http://csbi.mit.edu/events/annualsymposium/2006