Open Source Drug Discovery (OSDD) Open Lab


The Open Source Drug Discovery (OSDD) OpenLab conceptualizes novel approaches, explores novel computational methodologies and develops novel informatics toolkits to accelerate drug discovery for Neglected tropical diseases. The OpenLab is located at CSIR-IGIB Extension Center at Naraina.

Resources
The OSDD OpenLab maintains a number of relevant resources widely used by researchers across the world.

Internship Opportunities at OSDD OpenLab


Limited opportunities are available for Summer/Winter Interns in our lab. We usually take upto 5 interns every semester, while a larger (20-100) interns work on relevant problems online in close guidance. Typically the projects last fro 5-6 months. Please note that we would not be able to provide stipend/accommodation for the time period. To apply, please email to Dr. Vinod Scaria with "[openlab]" in the subject-line and a brief description of the problem you might be interested in working on.
Core Research Areas
We have in the past few years been exploring novel approaches towards assembling and integrating information from disparate resources towards understanding the biology of Mycobacterium tuberculosis and other pathogens. Our major focus areas are
  • Pathogen Genomics
  • Genome Annotation and Data Integration
  • Cheminformatics for neglected diseases
Focused Programmes
OSDD OpenLab has been one of the pioneers in crowd-sourcing for neglected tropical diseases through involving a large number of students and young researchers in genome-annotation and cheminformatics research.
Genes, Genomes and Genomics
The OSDD OpenLab has been maintaining the OSDD Open Access Repository of clinical isolates of Mycobacterium tuberculosis. A number of isolates from this repository has been sequenced and available in public domain.

A number of genomes from the OSDD Open Access Repository has been sequenced in Dr. Sridhar Sivasubbu Laboratory in collaboration. A complete list of the sequenced OSDD strains and publications are available here.


Selected Recent Publications
A number of student publications have arisen out of the work done at OSDD OpenLab. The recent list of selected publications are listed below. [Full list of Publications from the lab is available here]

Periwal V, Patowary A, Vellarikkal SK, Gupta A, Singh M, Mittal A, Jeyapaul S, Chauhan RK, Singh AV, Singh PK, Garg P, Katoch VM, Katoch, K, OSDD Consortium, Chauhan DS*, Sivasubbu S*, Scaria V*
Comparative Whole-Genome Analysis of Clinical Isolates Reveals Characteristic Architecture of Mycobacterium tuberculosis Pangenome
PLoS ONE (2015) Accepted

Periwal V, Scaria V*
Insights into structural variations and genome re-arrangements in prokaryotic genomes
Bioinformatics (2015) Jan 1;31(1):1-9. Epub 2014 Sep 4.

Sahajpal R, Kandoi G, Dhiman H, Raj S, OSDD Consortium, Scaria V, Bhartiya D and Hasija Y
HGV&TB: A comprehensive online resource on Human genes and genetic variants associated with Tuberculosis
Database (2014) Accepted

Jamal S, OSDD Consortium, Scaria V
Data-mining of potential antitubercular activities from molecular ingredients of Traditional Chinese Medicines 
PeerJ (2014) Accepted

Karuthedath Vellarikkal S, Patowary A, Singh M, Periwal V, Singh AV, Singh PK, Garg P, Mohan Katoch V, Katoch K, Jangir PK, Sharma R; Open Source Drug Discovery Consortium, Chauhan DS, Scaria V, Sivasubbu S.
Draft Genome Sequence of a Clinical Isolate of Multidrug-Resistant Mycobacterium tuberculosis East African Indian Strain OSDD271.
Genome Announc. 2013 Aug 1;1(4).

Jamal S, Periwal V, OSDD Consortium and Scaria V*

Predictive cheminformatics analysis of anti-malarial molecules inhibiting apicoplast formationBMC Bioinformatics 2013, 14:55 

Jamal S, Periwal V, OSDD Consortium, Scaria V*
Computational analysis and predictive modeling of small molecule modulators of microRNAJournal of Cheminformatics 2012, 4:16

Jamal S, Periwal V, OSDD Consortium, Scaria V*
Computational analysis and predictive modeling of small molecule modulators of microRNAJournal of Cheminformatics (2012), 4:16

Periwal V, Kishtapuram S, OSDD Consortium and Scaria V*
Computational models for in-vitro anti-tubercular activity of molecules based on high-throughput chemical biology screening datasets
BMC Pharmacology 2012, 12:1 

Periwal V, Jinuraj KR, OSDD Consortium, Jaleel UC* and Scaria V*
Predictive models for anti-tubercular molecules using machine learning on high-throughput biological screening datasets
BMC Research Notes 2011, 4:504