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Co-Sponsored by the Caltech Biological Network Modeling Center (BNMC)
Gustavo Kunde Rohde, Assistant Professor, Biomedical Engineering, Carnegie Mellon University
Monday, May 16, 2011
2:00 PM – 3:00 PM
Beckman Institute Auditorium
Novel biomedical imaging techniques have enabled the acquisition of quantitative information from cells, tissues, and organs with unprecedented accuracy and specificity. Combined with the availability of vast computational resources, quantitative biomedical imaging pipelines have the potential to accelerate scientific discovery and improve clinical practice. An important engineering problem in this area relates to extracting quantitative information related to the form (shape and texture) of cells, tissues, and organs. I will describe our recent efforts toward the development of a general purpose segmentation method and present preliminary evidence that a tool capable of high-enough accuracy for quantitative imaging pipelines may one day be available. In addition, recent efforts in developing geometric data analysis tools for mining morphological information from biomedical image data will be described. In particular, I will describe the application of deformation and transportation related metrics, in combination with discriminant analysis techniques, towards understanding the distribution of cellular patterns in cancerous and normal tissues.
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CACR Publication News: Cellcenter collaboration with developmental biologists yields insight in fruit fly genomics
“High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation” was published in the Genome Research Journal, Advanced Online Access, March 2011. Genome Research focuses on research that provides novel insights into the genome biology of all organisms, including advances in genomic medicine.
From the abstract:
“Cis-regulatory modules (CRMs) function by binding sequence specific transcription factors, but the relationship between in vivo physical binding and the regulatory capacity of factor-bound DNA elements remains uncertain. We investigate this relationship for the well-studied Twist factor in Drosophila melanogaster embryos by analyzing genome-wide factor occupancy and testing the functional significance of Twist occupied regions and motifs within regions … Our results show that high resolution in vivo occupancy data can be used to drive efficient discovery and dissection of global and local cis-regulatory logic.” (more)
CACR staff member Shirley Pepke analyzed the ChIP-seq binding data and found enhanced evolutionary conservation associated with candidate cis regulatory modules.
About Cellcenter: The goal of the Center for Integrative Study of Cell Regulation (Cell Center) is to develop new computational methods for understanding how the many genes and proteins that make up individual cells work together to carry out specialized functions of different cell types, including neurons, plant cells, and bacteria. See www.cellcenter.caltech.edu for further information.
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Cellcenter and SHC users now have access to the Intel Cluster Toolkit 3.2, including the compiler suite v 11.1. We have a two-seat license. “use intel” will this package into your environment. More Information about the Intel Cluster Toolkit
Pathscale compilers are being retired Feb 25, 2010. Users are encouraged to rebuild their codes using Intel, PGI, or gnu compilers. Specifically, these pathscale based packages will retire Feb 25:
- pathscale (alias for pathscale 3.2)
- pathscale_[3.1,3.2]
- openmpi_1.3.3_pathscale
- openmpi_1.3.3_pathscale_3.2
- openmpi_1.3.4_pathscale
- openmpi_1.4_pathscale
- openmpi_pathscale (alias for openmpi_1.3.3_pathscale_3.2)
Additional packages that will be retiring on Feb 25, due to bug fixes and newer release compatible offerings:
- openmpi_1.3.2 (alias for openmpi_1.3.2_gcc)
- openmpi_1.3.2_gcc
- openmpi_1.3.4_gcc
- openmpi_1.3.4_intel
- openmpi_1.3.4_pgi
- pgi_8.0
- tecplot-2006r2
- tecplot-2009r1
- totalview_8.6
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Wednesday, Sept 9, 2009
11:00 AM in 120 Powell Booth
Melaine Stefan
Computational Neurobiology Group
European Bioinformatics Institute (EBI)
Cambridge UK
