BIOCMS: Resource Integration and Web Application Framework for Bioinformatics

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8 Δεκ 2013 (πριν από 3 χρόνια και 8 μήνες)

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BIOCMS: Resource Integration and Web Application Framework for
Bioinformatics


DHUNDY R BASTOLA
†,
* , ANIL KHADKA

, MOHAMMAD SHAFIULLAH


AND HESHAM ALI
†,
*


College of Information Science and Technology, University of Nebraska at Omaha, Omaha, NE 68182
-
0116

*
Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198
-
6495


Abstract

High through put technologies in biomedical research allow for the study of biological processes as integrated systems. Signi
fic
ant amount of such data need to be stored, managed and analyzed to make the contribution of these data
meaningful. A resource facility comprising of members with diverse skill sets, including knowledge of programming and an educ
ati
onal background in biology will help in resource integration. This project exemplifies such relation that
exists between University of Nebraska at Omaha and other multiple INBRE units in Nebraska. The objective of current work was
to
develop a mechanism that allowed multiple researchers access constantly evolving hardware and
software resources that would aid in their biomedical research involving high
-
throughput data analysis. Custom application and f
unctionality were created under the open source web application framework called WebGUI. A prototype
framework (BIOlogical Content Management System) was developed that allows multiple users within INBRE units in Nebraska to u
plo
ad data, manage and use a collection of open
-
source and ‘in
-
house’ computational tools. The
features from the parent WebGUI simplify content management for users, while the versioning and workflow systems allow system

ad
ministrators to manage the system more efficiently. The development and availability of software
tailored to the needs of an individual laboratory will ensure data quality and enhance data analysis and discovery.



Motivation

Use of informatics tools in the analysis of biological data has become essential in many
biological fields. Biologists now use, in addition to spreadsheet, word processor and
statistical tools, many commercial and in
-
house
-
developed bioinformatics software for
sequence analysis, bio
-
data management, gene expression and proteomics. Most popular
tools include those which are accessible through the web. While more and more such
tools are available freely, it is not always easy to find the relevant ones. Biologists then
turn to Bioinformatics Core facility for help and often request the facilities to assemble a
list of such focused resources and make it available to their clientele. Motivated by this
need we developed a prototype framework (BIOlogical Content Management System) that
allows multiple users within INBRE units in Nebraska to upload data, manage and use a
collection of open
-
source and ‘in
-
house’ computational tools.

WebGUI

WebGUI is an open source content management system written in Perl and released under
the GNU General Public License. In WebGUI, creating and modifying web pages is done
with an intuitive browser
-
based system. Users have the freedom to create/modify content
fairly easily, have tools for sharing different files, and can choose different software to use
from a list of software that were either developed in
-
house or requested by the user or
deemed useful by the Bioinformatics Core Facility. This becomes an attractive feature for
Bioinformatics Core Service providers who have to deal with multiple users (defined as
groups) with similar needs but different content. This framework was especially attractive
for the following reasons:




Most customizable of the many CMS that is available.



Allow the ability to build and maintain complex website(s).



It is modular, pluggable and platform independent.



It is open source, well documented and supported.


Fig 2: (right
-
center and far
-
right) Integration of molecular biology laboratory inspired
features. Extension of WebGUI to incorporate requirements of researchers in the life
sciences. The screen shots shown include some of the available graphical user
interface in the BIOCMS for (A) Introduction to the research group (B) File sharing
between group members (C) Management of figures, graphs and pictures with
relevant captions (D) Collection of software available to group members (E) research
notebook supported by mediawiki and (F) genomic workflow management tool
-

Galaxy

Fig 1. (above) BIOCMS and relations between different components

(A)

(B)

(C)

(D)

(E)

(F)

BIOCMS Features


1.

User authentication


One user can belong to one or multiple groups with specific levels of privilege.


Access to content in BIOCMS is controlled by privileges assigned to the user.


All assets are separated based on groups.


2.

File sharing and management


Manuscripts and documents can be managed, organized and shared in
BIOCMS.


Users can view files being shared by group members and their attributes.


All files are maintained through a version controlling system to allow users to
easily revert to an older version of the file or retrieve deleted files just with a
few clicks.


File owners can control the attributes of a file and allow read
-
only access to
the file by other members.


Swish
-
e

indexing technology is used for advance searching. This technology
allows full indexing of DOC, PDF, HTML, plain text and Excel files.


3.

Software


Users have the option to choose from a list of in
-
house and third
-
party
software. An aesthetic, intuitive, and customizable dashboard is provided for
browsing the list of software.


Authentication modules have been developed for
a seamless user experience with
third
-
party software. It allows user authentication token can be passed to the
third
-
party software to avoid multiple login.


Software are categorized into ‘Group only’, ‘Group requested third
-
party’, and
‘Generic’.


A group notepad system is supported by Mediawiki technology and Galaxy
provides a genomic workflow management.

Acknowledgement

This project was supported by the NIH grant number P20 RR016469 from the
INBRE Program of the National Center for Research Resources.