Clc Bio Basic Company Presentation

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Clc Bio Basic Company Presentation

  1. 1. CLC bio Bioinformatics Solutions
  2. 2. Presentation of CLC bio <ul><li>HQ in Denmark. Offices in USA, Brazil & India, and resellers in 10+ countries </li></ul><ul><li>Focus on bioinformatics solutions: Software, Hardware, and Consulting services </li></ul><ul><li>A large number of world class bioinformatics scientists work for CLC bio </li></ul><ul><li>More than 47,000 software users since the first release in July 2005 </li></ul>
  3. 4. CLC bio – global reach CLC bio – global reach
  4. 5. Software objectives <ul><li>• To make user-friendly state-of-the-art bioinformatics software </li></ul><ul><li>• To integrate all analyses in one program </li></ul><ul><li>• To make software that works on: </li></ul><ul><li>• To involve users as much as possible </li></ul><ul><li>– CLC bio offers free user-support to all programs </li></ul><ul><li>– CLC bio is very open to user suggestions </li></ul><ul><li>– There are at least 2 program upgrades a year </li></ul>
  5. 6. CLC bio’s software solutions <ul><ul><li>CLC Free Workbench : A number of basic bioinformatics analyses, all integrated in the same software package. </li></ul></ul><ul><ul><li>CLC DNA Workbench : A large number of advanced DNA sequence analyses. </li></ul></ul><ul><ul><li>CLC RNA Workbench: Provides easy access to a range of complex algorithms and options, for RNA secondary structure prediction and editing. </li></ul></ul><ul><ul><li>CLC Protein Workbench : A large number of advanced protein sequence analyses. </li></ul></ul><ul><ul><li>CLC Combined Workbench : All the above gathered in one single, fully integrated software package. </li></ul></ul>
  6. 7. CLC Free Workbench <ul><li>Bioinformatics feature examples : </li></ul><ul><li>Multiple alignment </li></ul><ul><li>Phylogenetic trees </li></ul><ul><li>Restriction site finding </li></ul><ul><li>GenBank search </li></ul><ul><li>Viewing of all results from our commercial programs </li></ul>
  7. 8. CLC DNA Workbench <ul><li>Bioinformatics feature examples : </li></ul><ul><li>Assembly of DNA sequencing data ( Assembly) </li></ul><ul><li>Advanced primer design </li></ul><ul><li>Cloning </li></ul><ul><li>Automatic SNP annotation </li></ul><ul><li>Complexity region analyses </li></ul><ul><li>Dot plot based analyses </li></ul>
  8. 9. CLC RNA Workbench <ul><li>Bioinformatics feature examples : </li></ul><ul><li>Structure prediction </li></ul><ul><li>2D structure editor </li></ul><ul><li>Linear structure editor </li></ul><ul><li>RNA alignment </li></ul><ul><li>Pattern discovery </li></ul><ul><li>BLAST analysis </li></ul>
  9. 10. CLC Protein Workbench <ul><li>Bioinformatics feature examples : </li></ul><ul><li>Secondary structure predictions </li></ul><ul><li>BLAST searches (NCBI or Local) </li></ul><ul><li>Signal peptide prediction </li></ul><ul><li>3D molecule viewer </li></ul><ul><li>Transmembrane helix prediction </li></ul><ul><li>Hydrophobicity analyses </li></ul>
  10. 11. CLC Combined Workbench <ul><li>All the functionalities of Free, DNA, RNA and Protein in one program! </li></ul>
  11. 12. System requirements <ul><li>… for all workbenches from CLC bio: </li></ul><ul><li> </li></ul><ul><li>Mac OS X 10.3 or later (including Intel-based Macs) </li></ul><ul><li>Windows 2000, Windows XP, or Windows Vista </li></ul><ul><li>Linux: Redhat or SuSE </li></ul><ul><li>256 MB RAM required </li></ul><ul><li>512 MB RAM recommended </li></ul><ul><li>1024 x 768 display recommended </li></ul><ul><li>Additional requirements for CLC Protein Workbench and CLC Combined Workbench </li></ul><ul><li>3D viewing requires an OpenGL 3D graphics driver </li></ul>
  12. 13. CLC Software Developer Kit <ul><li>Software Developer Kit: This API enables the user to make his/her own modules for the CLC Workbench. </li></ul>
  13. 14. www.clccube.com
  14. 15. Hardware accelerated bioinformatics <ul><li>Acceleration through innovative use of FPGA technology </li></ul><ul><li>Smith-Waterman more than 100 times faster than a fast desktop computer </li></ul>
  15. 16. Hardware accelerated bioinformatics <ul><li>Portable: Plug-and-play connection through a USB 2.0 port </li></ul><ul><li>Upcoming: Faster Smith-Waterman searches, ClustalW, and other alignments </li></ul>
  16. 17. Cube Interfaces <ul><li>Blast interface </li></ul><ul><ul><li>Like NCBI Blast (including extension) </li></ul></ul><ul><ul><li>Add a command line parameter and the hardware Smith- Waterman is used </li></ul></ul><ul><ul><li>Easy integration with existing infrastructure </li></ul></ul><ul><li>Graphical interface </li></ul><ul><ul><li>Easy to use for all people </li></ul></ul><ul><ul><li>Better overview and workflow for Workbench users </li></ul></ul>
  17. 18. CLC Bioinformatics Cell
  18. 19. CLC Bioinformatics Cell <ul><li>Acceleration through innovative use of SIMD technology </li></ul><ul><li>Smith-Waterman more than 100 times faster than a fast desktop computer - speed depends on CPU-power </li></ul><ul><li>Current algorithms: Smith-Waterman and ClustalW </li></ul><ul><li>Upcoming:    - Even faster    - Significantly more algorithms    - Able to run in clusters </li></ul>
  19. 20. Some of CLC bio’s customers <ul><li>NASA Exobiology Branch, USA </li></ul><ul><li>National Institutes of Health (NIH), USA </li></ul><ul><li>Pasteur Institute, France </li></ul><ul><li>Royal Perth Hospital, Australia </li></ul><ul><li>National Hospital of Denmark </li></ul><ul><li>Solvay Pharmaceuticals, Germany </li></ul>“ The wide variety of other tools in CLC's software are extremely useful - BLAST searches from within the program, in silico restriction digests, alignments, phylogenetic trees, among a lot of other features.” Dr. Stefan J. Green, NASA, Exobiology branch.

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