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
●
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
The ScanMoment Project Objective
To
provide
on
-
line
tools
for
Bioinformatics
community
for
analysing
and
visualizing
the
protein
sequence
with
alpha
-
helix
moments
.
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
The User Interface Snapshots
The ScanMoment
Tabulated Output
The ScanMoment Graphical Output of 2bg9.pdb file
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
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
Mysql with the Netbeans
Connection from the Netbeans:
Services
-
> Databases
-
> jdbc:mysql://localhost:3306/dbname
Setting:
in my.cnf [mysqld] section: max_allowed_packet = 32MB
Subversion
–
version control system
Main 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
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
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
In the Netbeans tools
-
>options
-
>miscellaneous
-
versioning:
versioning system, the path, the repository connection
Netbeans : Manage Connection Setting
the connection to the central repository:
file:///home/netbeans/repository
svn+ssh://developmentSite/home/netbeans/repository
The Subversion from Netbeans: Search History
The
Subversion: Diff
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
Trac Installation
Requirements:
●
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)
●
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
The Trac setting
The Trac Snapshots ( Timeline )
The timeline lists:
creation and changes
ticket events
source code changes
milestone completed
creation and modifying
Wiki content
The Trac Snapshots ( Roadmap )
The RoadMap shows the
road ahead, using upcoming
milestones
The Trac Snapshots( Browse Source )
The Trac Snapshots ( View Tickets )
The Ticket View provides
tracking of issues and bugs
within a project
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.
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
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
Enter the password to open this PDF file:
File name:
-
File size:
-
Title:
-
Author:
-
Subject:
-
Keywords:
-
Creation Date:
-
Modification Date:
-
Creator:
-
PDF Producer:
-
PDF Version:
-
Page Count:
-
Preparing document for printing…
0%
Commentaires 0
Connectez-vous pour poster un commentaire