The ScanMoment Project Presentation The development team:

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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
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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

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

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The User Interface Snapshots
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The ScanMoment Tabulated Output
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The ScanMoment Graphical Output of 2bg9.pdb file
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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 software
  development projects

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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

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Mysql with the Netbeans
Setting in my.cnf mysqld
section max_allowed_packet 32MB
Connection from the Netbeans Services -gt
Databases -gt jdbcmysql//localhost3306/dbname
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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

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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

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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 ltfiles or
  projectgt
• examine your changes
  diff ltversion1,
  version2gt
• revert your changes
  revert ltfile or projectgt
  
• status
  

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In the Netbeans tools-gtoptions-gtmiscell
aneous-versioning versioning system, the path,
the repository connection
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Netbeans Manage Connection Setting
the connection to the central repository
file///home/netbeans
/repository
svnssh//developmentSite/home/netbeans
/repository
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The Subversion from Netbeans Search History
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The Subversion Diff
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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

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Trac Installation
Requirements

• python v gt 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)
  
  

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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 developmentSite8000 and
  ltLocationgt section
• resynchronize the Trac against the repository
  
• trac-admin /srv/trac/ resync
  
  

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The Trac Snapshots ( Timeline )
The timeline lists creation and changes
ticket events source code changes
milestone completed creation and modifying
Wiki content
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The Trac Snapshots ( Roadmap )
The RoadMap shows the road ahead, using upcoming
milestones
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The Trac Snapshots( Browse Source )
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The Trac Snapshots ( View Tickets )
The Ticket View provides tracking of issues
and bugs within a project
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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.

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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

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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