From csbi-events at mit.edu Tue Sep 6 16:25:21 2005 From: csbi-events at mit.edu (csbi-events@mit.edu) Date: Tue, 6 Sep 2005 16:25:21 -0400 Subject: [CSBi-events] Save the date for CSBi Seminars Message-ID: SAVE THE DATE! SAVE THE DATE! Fall 2005 Seminar Series on Computational and Systems Biology September 23, 2005 Andrew Emili, University of Toronto, Program in Proteomics & Bioinformatics Hosted by Forest White October 21, 2005 Philip Green, University of Washington, Genome Sciences Hosted by Chris Burge November 4, 2005 Carla Mattos, North Carolina State University, Molecular and Structural Biochemistry Hosted by Bruce Tidor November 18, 2005 Peter Sorger, Massachusetts Institute of Technology, Biology Hosted by Chris Burge December 2, 2005 Daniel Herschlag, Stanford University, School of Medicine, Beckman Center Hosted by David Bartel December 9, 2005 Benjamin Blencowe, University of Toronto, Medical Genetics and Microbiology Co-hosted by Phil Sharp and Chris Burge Fridays 3:00-4:00 p.m MIT 4-270 - Maclaurin Building Light refreshments to be served at 2:45 p.m. More information can be found at http://csbi.mit.edu Contacts: Prof. Chris Burge, cburge at mit.edu, 617-258-5997 and Brenda Pepe, pepebe at mit.edu, 617-452-3885 From csbi-events at mit.edu Wed Sep 7 09:23:48 2005 From: csbi-events at mit.edu (csbi-events@mit.edu) Date: Wed, 7 Sep 2005 09:23:48 -0400 Subject: [CSBi-events] Mark Your Calendars Message-ID: Dear CSBi Members: Please mark your calendars for a special CSBi seminar: TOM LAUE. Professor of Biochemistry and Molecular Biology, UNH Director, The Center to Advance Molecular Interaction Science Director, Biomolecular Interactive Technology Center Title: "Protein charge and protein behavior in concentrated solutions" Date: Wednesday, September 14 Time: 2:00-3:00 p.m. Place: Bldg 68, Room 180 -- 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 Wed Sep 7 10:12:31 2005 From: csbi-events at mit.edu (csbi-events@mit.edu) Date: Wed, 07 Sep 2005 10:12:31 -0400 Subject: [CSBi-events] New course: 6.095/6.895: Computational Biology: Genomes, Networks, Evolution Message-ID: <6.2.1.2.2.20050907093146.025a5c60@hesiod> New course Fall 2005: 6.095(U) / 6.895(G) Computational Biology: Genomes, Networks, Evolution Profs. Manolis Kellis and Piotr Indyk http://compbio.mit.edu/6.895/ Lectures: TR11-12:30 in 3-370 Covers the algorithmic and machine learning foundations of computational biology, combining theory with practice. We study the principles of algorithm design for biological datasets, and analyze influential problems and techniques. We use these to analyze real datasets from large-scale studies in genomics and proteomics. Topics include: * Genomes: Biological sequence analysis, hidden Markov models, gene finding, RNA folding, sequence alignment, genome assembly. * Networks: Gene expression analysis, regulatory motifs, graph algorithms, scale-free networks, network motifs, network evolution. * Evolution: Comparative genomics, phylogenetics, genome duplication, genome rearrangements, evolutionary theory, rapid evolution. First class meets on Thursday Sept 8 at 11am in 3-370. More Information: http://compbio.mit.edu/6.895/ TA: Pouya Kheradpour Units: 3-0-9 Prerequisites: 6.001, 7.01, 6.041 Engineering Concentration: Theory of Computer Science Course numbers: 6.095 (U): Undergraduate version. Includes midterm, final project. No final exam. 6.895 (G): The graduate version of the course includes additional assignments, a more ambitious final project, which can lead to a thesis / publication. From csbi-events at mit.edu Wed Sep 14 12:04:15 2005 From: csbi-events at mit.edu (csbi-events@mit.edu) Date: Wed, 14 Sep 2005 12:04:15 -0400 Subject: [CSBi-events] None Message-ID: New Course! New Course! New Course! New Course! New Course! New Course! STARTS SEPT 15, 2005 2.996J/BE.949J Optical Microscopy and Spectroscopy for Biology and Medicine Drs. Peter So and Colin Sheppard Tuesday and Thursday 8:00am-9:30 am Room 8-404 Introduces the theory and the design of optical microscopy and its applications in biology and medicine. The course starts from an overview of basic optical principles allowing an understanding of microscopic image formation and common contrast modalities such as dark field, phase, and DIC. Advanced microscopy imaging techniques such as total internal reflection, confocal, and multiphoton will also be discussed. Quantitative analysis of biochemical microenvironment using spectroscopic techniques based on fluorescence, second harmonic, Raman signals will be covered. We will also provide an overview of image processing techniques for microscopic data. Prereq: permission of instructor 3-0-9 H-Level Grad Credit http://stellar.mit.edu/S/course/2/fa05/2.996/index.html -- 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 Sep 15 11:26:44 2005 From: csbi-events at mit.edu (csbi-events@mit.edu) Date: Thu, 15 Sep 2005 11:26:44 -0400 Subject: [CSBi-events] Mark Your Calendar Message-ID: High Performance Deconvolution and Effects on Downstream Image Analysis Hans van der Voort, Ph.D. CEO & CSO, Scientific Volume Imaging The Netherlands 10.30 am Thursday September 29th McGovern Auditorium, Whitehead Contact: James G. Evans (jgevans at wi.mit.edu) Abstract: Deconvolution aims to recover the 'true' object distribution from an image distorted by, among others, diffraction and noise. The resolution measured in terms of the Half Intensity Width (HIW) in deconvolved images can be much higher than in the original, under ideal conditions near-isotropic sub-100nm HIW values can be achieved. However, in confocal or two-photon fluorescence microscopy the available signal strengths do not allow such extremely high HIW values, but there deconvolution can significantly improve the axial resolution, while effectively reducing noise. The introduction in recent years of fast Nipkow disk based confocal microscopes has made it possible to acquire large 3D-time series. On top of that, the number of voxels per 3D image frame is steadily increasing. Since deconvolution is generally a compute intensive procedure these two ongoing developments result in a rapidly growing demand for high performance deconvolution systems. In this talk we will discuss high performance deconvolution algorithms and their effect on resolution. In addition the effect of deconvolution on the reliability of co-localization coefficients will be discussed in detail. -- 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 Sep 16 08:59:48 2005 From: csbi-events at mit.edu (csbi-events@mit.edu) Date: Fri, 16 Sep 2005 08:59:48 -0400 Subject: [CSBi-events] CSBi Seminar Series - Dr. Andrew Emili Message-ID: Dr. Andrew Emili University of Toronto Department of Medical Genetics and Microbiology Trawling the Interactome: New Analytical Approaches for Old Problems Abstract The Emili laboratory develops, evaluates and applies advanced cross-disciplinary proteomic methods to investigate the function and mechanistic integration of the complex biochemical circuitry that underlies cell growth and proliferation. In this talk, I will discuss our latest experimental procedures for high-throughput protein mass spectrometry, affinity purification and biochemical fractionation as a means for examining the global molecular machineries of model systems ranging from E. coli and budding yeast, to mouse and human. I will also explore our group's efforts to develop an integrated informatics platform to mine these genome-scale datasets for biological insight. Friday, September 23, 2005 Maclaurin Building (4-270) 3:00 - 4:00 p.m. Light refreshments served at 2:45 p.m. Host: Dr. Forest White Biological Engineering Contact: Brenda Pepe, 2-3885 http://csbi.mit.edu/ Sponsored by CSBi Annual CSBi Seminar Series in Computational and Sysems Biology -- Brenda E. Pepe Administrative Assistant to Professor Christopher B. Burge Massachusetts Institute of Technology Department of Biology, 68-223 31 Ames Street Cambridge, MA 02139 Tel: 617-452-3885 Fax: 617-452-2936 From csbi-events at mit.edu Wed Sep 28 08:08:22 2005 From: csbi-events at mit.edu (csbi-events@mit.edu) Date: Wed, 28 Sep 2005 08:08:22 -0400 Subject: [CSBi-events] CSBi Seminar - High Performance Deconvolution Imaging Message-ID: High Performance Deconvolution and Effects on Downstream Image Analysis Hans van der Voort, Ph.D. 10:30am , Thursday, September 29th McGovern Auditorium, Whitehead Institute Deconvolution aims to recover the 'true' object distribution from an image distorted by, among others, diffraction and noise. The resolution measured in terms of the Half Intensity Width (HIW) in deconvolved images can be much higher than in the original, under ideal conditions near-isotropic sub-100nm HIW values can be achieved. However, in confocal or two-photon fluorescence microscopy the available signal strengths do not allow such extremely high HIW values, but there deconvolution can significantly improve the axial resolution, while effectively reducing noise.The introduction in recent years of fast Nipkow disk based confocal microscopes has made it possible to acquire large 3D-time series. On top of that, the number of voxels per 3D image frame is steadily increasing. Since deconvolution is generally a compute intensive procedure these two ongoing developments result in a rapidly growing demand for high performance deconvolution systems. In this talk we will discuss high performance deconvolution algorithms and their effect on resolution. In addition the effect of deconvolution on the reliability of co-localization coefficients will be discussed in detail. Contact: James G. Evans (jgevans at wi.mit.edu)