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DON'T PUT A COMMENT ! -- Bioinformatics at the HPCf :: ----- this is a comment ---------------------------------------------------- Introduction Bioinformatics: the application of computer technology to the study of biological systems. :: ---------------------------------------------------------------------------- UPR High Performance Computing facility A shared facility supporting research in all campuses and units of the UPR. See our webpage at !hhttp://www.hpcf.upr.edu/ for more information. We have 3 main areas: Center for Numerical Supercomputing HPCf VizLab Internet2 GigaPOP Bioinformatics Resource Center (BiRC) :: ---------------------------------------------------------------------------- Center for Numerical Supercomputing Funded by EPSCoR home to several sgi Origin 2000 shared memory supercomputers two 8 processor and one 24 processor our largest machine has 24 processors, 19.2 GB RAM, 500 GB Disk space :: --- HPCf VizLab Funded by NSF sgi Onyx2 visualization supercomputer two Infinite Reality 2 graphics pipes combined with Origin 2000 total 24 processors, 19.2 GB RAM two teaching labs (Mayaguez and HPCf) five sgi O2 workstations five sgi 230 linux workstations dual LCD projectors large format printers digital video editing facilities :: --- Internet2 GigaPOP Funded by NSF Internet2 network to connect UPR-RRP, UPR-RCM, UPRM, Arecibo Radiotelescope Very high speed links (155Mbps, 100 times a T1) Private network only for research institutions Internet2 contract awarded to Centennial/Qwest see !hhttp://internet2.centennialpr.com/ !hhttp://www.qwest.com:80/about/media/pressroom/1,1720,402_archive,00.html :: ---------------------------------------------------------------------------- Bioinformatics Resource Center (BiRC) Funded by PR-BRIN home to sgi Origin 300 shared memory supercomputer (cafeina) 24 GB RAM, 32 Processors espresso linux cluster 172 Xeon 2.4 GHz, 85 GB RAM, Gigabit ethernet :: --- Bioinformatics at the HPCf See our website !hhttp://www.hpcf.upr.edu/biology/ for the latest information Publication alerts Sequence analysis Phylogeny Protein structure Microarrays Custom Programming :: --- Publication Alerts The biomail service can notify you of new pubmed entries that match specific keywords. You can store several searches under one email account Searches can be mailed monthly or up to twice a week Available at !hhttp://biomail.hpcf.upr.edu/cgi-bin/biomail/users.pl :: ---------------------------------------------------------------------------- Sequence Analysis Client based tools Sequence Manipulation Suite mirror lightweight javascript based sequence analysis tools run in your browser with javascript you can mirror them in your lab available at !hhttp://biology.hpcf.upr.edu/sms/ :: --- Sequence Analysis (continued) Unix tools Wisconsin Package (gcg) Consists of 130+ integrated programs !hwww.hpcf.upr.edu/biology/gcghelp/short_descriptions.html Currently available at the HPCf Requires a research account on our supercomputer Command-line and X Window System versions available See !hwww.gcg.com or !hwww.hpcf.upr.edu/biology/gcg.html :: --- Phylogeny Packages PAUP (in gcg) Only for sequence based phylogeny. The phylip package version 3.6 34 programs for phylogenetic analysis sequence analysis discrete characters continuous characters :: --- Genetic Linkage & Mapping fastlink - Faster version of the Linkage suite BPE - meiotic breakpoint mapping for genetic and radiation-hybrid mapping TkMap - Publication quality linear maps :: --- Protein Structure Molecular Dynamics - model protein structures EGO - model up to 40,000 atoms NAMD - Integrate modeling and viewing with VMD MMTK - molecular modeling toolkit, build your own models Structure viewers Rasmol Visual Molecular Dynamics (vmd) !hhttp://www.ks.uiuc.edu/Research/vmd/ :: --- Microarrays !iscatter.png :: --- Custom Programming The HPCf has programming staff with experience in many areas sequence analysis: bioperl, biopython graphics: biowidgets for Tk, OpenGL, java, VTK genetic mapping: BPE, TkMap, fastlink, linkage microarray analysis: custom python programs, GENECLUSTER, Atlas ImageArray modeling biological systems: fortran, C, C++ :: --- Additional Resources I maintain a computational biology link page with pointers to many more bioinformatics resources. !hhttp://www.hpcf.upr.edu/~humberto/cmb/ :: --- About this presentation The presentation was prepared with slides.sh, available from: !hhttp://fx.lebail.free.fr/slides-latest.tar.gz The presentation is at: !hhttp://www.hpcf.upr.edu/~humberto/slides.sh/bioinformatics/ The source of the presentation is available here: !lhttp://www.hpcf.upr.edu/~humberto/slides.sh/bioinformatics/source.txt