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The ScanMoment Project Presentation The development team:

The ScanMoment Project Presentation The development team:. Dr. Steven E. Massey (Biology assistant Prof.) Tessa Humphries-Beckley (Biology PhD) Alejandro Medina (Computer Science) Elena Leyderman (HPCf). HPCf at University of Puerto Rico by Elena Leyderman March 2010. Outline.

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The ScanMoment Project Presentation The development team:

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  1. The ScanMoment Project PresentationThe development team: • Dr. Steven E. Massey (Biology assistant Prof.) • Tessa Humphries-Beckley (Biology PhD) • Alejandro Medina (Computer Science) • Elena Leyderman (HPCf) HPCf at University of Puerto Rico by Elena Leyderman March 2010

  2. Outline • The project objective, it's main features and its short description and snapshots • Technologies used in the project and their description • Current status of the project and the future plans • Conclusion

  3. The ScanMoment Project Objective To provide on-line tools for Bioinformatics community for analysing and visualizing the protein sequence with alpha-helix moments.

  4. The ScanMoment Project Features • The ScanMoment is a web server • Searches for alpha-helix motifs in a protein sequences • Protein sequence can be read from a line, or from a file in a pdb format (local or via URL from the RCSB databank) • Protein sequences and calculated moments are stored in a mysql database to avoid repetition of time-consuming parsing and calculations • The output is provided: in a tabulated form as a plot as a 3D animated structure

  5. The User Interface Snapshots

  6. The ScanMomentTabulated Output

  7. The ScanMoment Graphical Output of 2bg9.pdb file

  8. Open Source Technologies used in the ScanMoment • Netbeans 6.8 • Java JDK 1.6 • Apache Tomcat 6.0.20 Web server • Mysql 5.0.77- 4 • JMol – 3D viewer of chemical structures • Subversion 1.4.2-4 -version control system • Trac 0.11– tracking system for softwaredevelopment projects

  9. Netbeans – a software integrated development environment Main Features • available for all main OS. • includes an editor, profiler, debugger, database drivers • supports collaborative tools, like version control systems • default language – java, support for -php, javaScript, ruby, python, groovy, C, C++ • allows developing web pages, servlets, webservices, desktop applications • it comes with a choice of web servers: the ClassFish or the Apache Tomcat • allows to create project documentation: shows all classes, it's functions, inserts source code comments

  10. Mysql with the Netbeans Setting: in my.cnf [mysqld] section: max_allowed_packet = 32MB Connection from the Netbeans: Services -> Databases -> jdbc:mysql://localhost:3306/dbname

  11. Subversion – version control systemMain Features • cross – platform • the central repository and independent working copies • operates across network • synchronization between developers • atomic commits (it cannot go partially) • versioning for any kind of files, directories, and metadata (properties) • full revision history

  12. The Subversion Setting • install the Subversion on each computer: svn –exectable and svnadmin – administrative tool • create empty repositories: svnadmin create /home/netbeans/repository (central repository) svnadmin create /home/netbeans/elena (local repository) • the initial checkout to create a working copy in the local repository • in the Netbeans specify the connection to the Subversion

  13. Basic Subversion Command-lines • create a working copy from a central repository: checkout http://developmentSite/repository • bring up to date (or an old) version: update [to an old version] • publish your changes: commit <files or project> • examine your changes: diff <version1, version2> • revert your changes: revert <file or project> • status

  14. In the Netbeans tools->options->miscellaneous-versioning: versioning system, the path, the repository connection

  15. Netbeans : Manage Connection Setting the connection to the central repository: file:///home/netbeans/repository svn+ssh://developmentSite/home/netbeans/repository

  16. The Subversion from Netbeans: Search History

  17. The Subversion: Diff

  18. The Trac - project management and tracking system Main Features • has a buid-in Wiki engine • provides a link between: svn, internal database and wiki content • serves as a web interface to svn • timeline of all recent activity • roadmap • ticket system • customizing reports • multiple project support • fine grained permissions • email notification

  19. Trac InstallationRequirements: • python v >= 2.3 and some its utilities pygments - to highlight syntax pytz - to get list of time zones misc - to analyze webserver log genshi - generate web output • a database (mysql) • a revision control system (svn) • a web server (apache)

  20. The Trac setting • the installation results in: tracd and trac-admin • creating a backend Trac storage available for apache user: wiki pages, tickets, reports, settings and the repository • trac-admin /srv/ initenv • set svn repository to trac repository • create account in apache subdirectory of the Trac path: • htpasswd -c /srv/apache/htpasswd elena • create user permissions, like TRAC_ADMIN or Road_MAP_VIEW etc.: • trac-admin /srv/ permissions add alejandro TRAC_ADMIN • configure apache (httpd.conf): • Listen: developmentSite:8000 and <Location> section • resynchronize the Trac against the repository • trac-admin /srv/trac/ resync

  21. The Trac Snapshots ( Timeline ) The timeline lists: creation and changes ticket events source code changes milestone completed creation and modifying Wiki content

  22. The Trac Snapshots ( Roadmap ) The RoadMap shows the road ahead, using upcoming milestones

  23. The Trac Snapshots( Browse Source )

  24. The Trac Snapshots ( View Tickets ) The Ticket View provides tracking of issues and bugs within a project

  25. Jmol Viewer - Java viewer for chemical structures in 3D Jmol features: • can be integrated into web pages • cross-platform: Windows, Unix, Mac • javaScript support library • support for all major web browsers • 3D rendering (no hardware requirements) • animations • measurements • very wide list of file formats • export to image files, pdf,web page etc.

  26. Our Future Plans • implement a new GUI • handling exceptions • create interaction between plots and jmol applet • get the entire RCSB protein data bank in the ScanMoment database and update it regularly • implement new algorithms

  27. Conclusion • the scanMoment is implemented as a web server accessible via www.scanmoment.org • it is intended to be a convenient online tool for identifying alpha helix motifs in proteins • it's written in Java using the Netbeans development environment. • nice collaborative tools are used to provide a convenient way for managing our project implemented by a team of dispersed developers • the future work is intended to provide the better user interface, interaction, and add further analyses of protein structure

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