1. Unipro UGENE: an open-source toolkit for complex genome analysis Konstantin Okonechnikov, Novosibirsk State University Olga Golosova, Alexey Varlamov, Mikhail Fursov Unipro Company

2. Unipro UGENE project What is UGENE? A multiplatform open-source application for molecular biologists Project goal: Quality integration of popular bioinformatics tools into the unified visual and computational solution History Started 5 years ago as years ago as a set of small collaborative projects with several academic organizations For last 3 years rapidly developed due to the Unipro company support Winner of several global Russian competitions

3. UGENE internals Written in C++/Qt Modular structure Integrated plugin system Automated testing > 4000 tests UGENE “Core” team: Mostly graduates of Novosibirsk State University Have professional skills in bioinformatics and software development

4. UGENEfeatures: algorithms Rich library of popular bioinformatics algorithms and computational methods Smith-Waterman, Clustal, Muscle, KAlign, Blast, Phylip, HMM, Primer3, Psipred, Bowtie, UGENE Genome Aligner… + several dozens more Some algorithms are unique: contributed by local research labs and academia

5. UGENEfeatures: data formats Support of popular biological data formats (~ 20 formats) FASTA, Genbank, Stockholm, PDB, Newick, Nexus(Mega), ClustalW, SAM, BAM… Retrieve information from remote databases: NCBI, PDB, Swissprot…

6. UGENE features: visualization Sequence View Annotation Editor Sequence Circular view Multiple Alignment Editor Biopolymer 3D viewer Assembly Browser (new!) etc

8. NVidia CUDA version > 10x faster on GPUOptimized algorithms examples: UGENE features: HPC

9. UGENE Workflow Designer Visual environment for constructing computational workflows Joining all together Rich algorithm libraries Unified data formats Powerful user interface High performance

10. Main Toolbar Elements Library Workflow Scene Element Properties UGENE Workflow Designer

11. Workflow Designer Features Internal data model: no data input/output conversion Parameters can be customized with scripts Easy local usage: no any additional configuration required Support for launching workflows on remote computational resources

12. Create new shell command from workflow Use your own workflow as a stand alone command line tool Example: ugene align --in=file1.aln –-out=file2.ali Where ‘align’ is the name of the workflow ‘--in’ and ‘--out’ are cmd-line aliases for workflow parameters Reusing workflows

13. Easy extending workflows Script new features Use embedded scripting language нo design new workflow building blocks Customize elements parameters with scripts Add external tools (new in 1.9.4!) Create custom workflow elements by configuring input and output of a an external program or script

14. UGENE: future plans Web environment for workflow designer View & share workflows Launch workflows on cloud resources Support for NGS data analysis New algorithms: align, assembly, SNP/indels BAM viewer

15. UGENE community Over 500 downloads every month, users all over the world Included into major Linux distributions: Ubuntu, Fedora, SUSE etc… Issue tracker, forum, SVN (links on next slide) New members are welcome!

16. Questions Thank you for your attention! Useful links Website: http://ugene.unipro.ru Issue tracker: https://ugene.unipro.ru/tracker Board: http://ugene.unipro.ru/forum/ SVN: https://ugene.unipro.ru/svn/ugene/ UGENE team e-mail: ugene@unipro.ru