The ScanMoment Project Presentation The development ...

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