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Unipro ugene bosc 2011 update

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Unipro ugene bosc 2011 update

  1. 1. Unipro UGENE: an open-source toolkit for complex genome analysis<br />Konstantin Okonechnikov, <br />Novosibirsk State University<br />Olga Golosova, Alexey Varlamov, Mikhail Fursov<br />Unipro Company<br />
  2. 2. Unipro UGENE project<br />What is UGENE?<br />A multiplatform open-source application for molecular biologists<br />Project goal: <br />Quality integration of popular bioinformatics tools into the<br />unified visual and computational solution<br />History<br />Started 5 years ago as years ago as a set of small collaborative projects with several academic organizations<br />For last 3 years rapidly developed due to the Unipro company support <br />Winner of several global Russian competitions<br />
  3. 3. UGENE internals<br />Written in C++/Qt<br />Modular structure<br />Integrated plugin system <br />Automated testing<br /> > 4000 tests<br />UGENE “Core” team:<br />Mostly graduates of Novosibirsk State University<br />Have professional skills in bioinformatics and software development<br />
  4. 4. UGENEfeatures: algorithms<br /> Rich library of popular bioinformatics algorithms and computational methods <br />Smith-Waterman, Clustal, Muscle, KAlign, Blast, Phylip, HMM, Primer3, Psipred, Bowtie, UGENE Genome Aligner…<br />+ several dozens more<br /> Some algorithms are unique: contributed by local research labs and academia<br />
  5. 5. UGENEfeatures: data formats<br />Support of popular biological data formats (~ 20 formats)<br />FASTA, Genbank, Stockholm, PDB, Newick, Nexus(Mega), ClustalW, SAM, BAM… <br />Retrieve information from remote databases:<br />NCBI, PDB, Swissprot…<br />
  6. 6. UGENE features: visualization<br />Sequence View <br />Annotation Editor<br />Sequence Circular view<br />Multiple Alignment Editor<br />Biopolymer 3D viewer<br />Assembly Browser (new!)<br />etc<br />
  7. 7. Optimization for existing algorithms<br />Multi-core CPU<br />Special instructions (SSE etc)<br />GPU<br />Support for launching computational tasks on clusters and clouds<br />HMMER2:<br /><ul><li>30x faster on Intel Core 2 Quad</li></ul>Smith-Waterman:<br /><ul><li>3x faster on SSE2-capable CPUs
  8. 8. NVidia CUDA version > 10x faster on GPU</li></ul>Optimized algorithms examples:<br />UGENE features: HPC<br />
  9. 9. UGENE Workflow Designer<br />Visual environment for constructing computational workflows<br />Joining all together<br />Rich algorithm libraries<br />Unified data formats<br />Powerful user interface<br />High performance<br />
  10. 10. Main Toolbar<br />Elements Library<br />Workflow Scene<br />Element Properties<br />UGENE Workflow Designer<br />
  11. 11. Workflow Designer Features<br />Internal data model: no data input/output conversion<br />Parameters can be customized with scripts<br />Easy local usage: no any additional configuration required <br />Support for launching workflows on remote computational resources<br />
  12. 12. Create new shell command from workflow<br />Use your own workflow as a stand alone command line tool<br />Example: ugene align --in=file1.aln –-out=file2.ali<br />Where<br />‘align’ is the name of the workflow<br />‘--in’ and ‘--out’ are cmd-line aliases for workflow parameters<br />Reusing workflows<br />
  13. 13. Easy extending workflows<br />Script new features <br />Use embedded scripting language нo design new workflow building blocks<br />Customize elements parameters with scripts<br />Add external tools <br />(new in 1.9.4!) <br />Create custom workflow elements by configuring input and output of a an external program or script<br />
  14. 14. UGENE: future plans<br />Web environment for workflow designer<br />View & share workflows<br />Launch workflows on cloud resources<br />Support for NGS data analysis<br />New algorithms: align, assembly, SNP/indels<br />BAM viewer<br />
  15. 15. UGENE community<br />Over 500 downloads every month, users all over the world<br />Included into major Linux distributions: Ubuntu, Fedora, SUSE etc…<br />Issue tracker, forum, SVN (links on next slide)<br />New members are welcome!<br />
  16. 16. Questions<br />Thank you for your attention!<br />Useful links<br />Website: http://ugene.unipro.ru<br />Issue tracker: https://ugene.unipro.ru/tracker<br />Board: http://ugene.unipro.ru/forum/<br />SVN: https://ugene.unipro.ru/svn/ugene/<br />UGENE team e-mail: ugene@unipro.ru<br />

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