The ScanMoment Project Presentation The development ...

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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

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