BOL: Related items

Enrichr: a comprehensive gene set enrichment analysis

Jit — Thu, 27 Apr 2017 05:42:09 -0500

Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools in this domain called Enrichr. Enrichr currently contains a large collection of diverse gene set libraries available for analysis and download. In total, Enrichr currently contains 180 184 annotated gene sets from 102 gene set libraries. New features have been added to Enrichr including the ability to submit fuzzy sets, upload BED files, improved application programming interface and visualization of the results as clustergrams. Overall, Enrichr is a comprehensive resource for curated gene sets and a search engine that accumulates biological knowledge for further biological discoveries. Enrichr is freely available at: http://amp.pharm.mssm.edu/Enrichr.

https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkw377

Address of the bookmark: http://amp.pharm.mssm.edu/Enrichr/

Bioinformatics Programme Officer @ International Centre for Genetic ICGEB Engineering and Biotechnology

Fri, 23 Nov 2018 03:50:16 -0600

The following vacancies are available in the DBT Apex Biotechnology Information project at ICGEB, New Delhi, India. These positions are available for a period of approx. two years, however, initial appointment offer will be for 6 months, which will be extended based on performance of work. Salaries will be offered as per DBT, educational qualification and experience. Depending on requirements, selected candidates may be required to work on location from the Department of Biotechnology, New Delhi. Shortlisted candidates will be invited for an interview at ICGEB. Only the selected candidates will be informed individually. No TA/DA or accommodation will be offered to the candidates attending the interview.

4 Programme Officer 1
5 Technical Research Assistant 1

Minimum Educational Qualification, desirable experience and expected duties:

4: The applicants should be Postgraduates with experience in Data collection and Statistics, especially in Biotechnology-related data.

Expected duties: Collection of Biotechnology related information from India, to facilitate the Apex BTIC experts committee review of programmes at centres and R&D programs funded by DBT.

5: The applicants should be Postgraduates in Science with experience in Bioinformatics-related projects.
Expected duties: The candidates will assist the senior staff of the centre in daily activities and help in the preparation of the Annual Training Calendar, seminar and training podcasts/videos, repository of training material and Apex BTIC Newsletter.

Interested candidates should submit their full, updated Curriculum Vitae with a detailed description of relevant experience, along with two references by December 14th, 2018, addressed to, The Chairperson, DBT- Apex BTIC, ICGEB, Aruna Asaf Ali Marg, New Delhi 110067, Email: abtic@icgeb.res.in, kindly write “Application for DBT Apex BTIC vacancy” in the subject of the email or envelope, if sending by post.

Advertisement: http://www.icgeb.org/tl_files/Vacancies/dbt-abtic-vac-annmntrevsk.pdf

Covid Spectrum !

Abhi — Sun, 25 Sep 2022 18:56:47 -0500

https://cov-spectrum.org/explore/World/AllSamples/

Address of the bookmark: https://cov-spectrum.org/

UCSC SARS-CoV-2 Genome Browser

Jit — Thu, 06 Jan 2022 06:48:40 -0600

The UCSC SARS-CoV-2 Genome Browser (https://genome.ucsc.edu/covid19.html) is an adaptation of our popular genome-browser visualization tool for this virus, containing many annotation tracks and new features, including conservation with similar viruses, immune epitopes, RT–PCR and sequencing primers and CRISPR guides. We invite all investigators to contribute to this resource to accelerate research and development activities globally.

Address of the bookmark: https://www.nature.com/articles/s41588-020-0700-8

SCFBio have developed Sanjeevini

Jit — Fri, 17 Nov 2017 07:55:49 -0600

SCFBio have developed a new android based application for drug design called Sanjeevini (https://play.google.com/store/apps/details?id=com.sanjeevini&hl=en). It is available free of charge. You can download it using Google play store. Just search for "Sanjeevini-SCFBIO-CADD" in Google play store. It contains all modules used by current Sanjeevini users. We have worked towards making a unified and easy to use interface. The app now supports all major small molecule file formats (pdb, mol, sdf, mol2 and xyz). The application contains inbuilt visualizer JSmol for easy analysis of results. Users can now directly download the protein files from PDB ("Get protein PDB file" in `FILE` Menu) and prepare it using the easy to use in-built module "Prepare protein/DNA".

SCFBio have worked towards making the process of Job retrieval more streamlined and user friendly. All jobs are now recorded in the "Job results". It can be accessed using the main page of the application. Job status can now be retrieved by clicking on the refresh button against the job ID.

SCFBio have also added a new feature of accessing Jobs run on different android application. Users can retrieve jobs run by other users by sharing the job ID and module name. This feature can be accessed using the Import Jobs option in File menu. We hope this feature will help collaborating groups stay in touch with each other.

The module contains all modules of Sanjeevini suite of software for structure based Drug design.

Sl No.	Module name	Activity
1	Prepare Protein/DNA	Prepares protein/DNA for other modules of Sanjeevini
2	Prepare ligand	Prepares ligands for other modules of Sanjeevini
3	Active site Prediction	Predicts biologically relevant sites in a protein
4	ParDOCK	Rigid Docking of Protein-Ligand complex
5	BAPPL	Binding affinity prediction of Protein-Ligand complex
6	BAPPL Z	Binding affinity prediction of Protein-Zinc-Ligand complex
7	DNA ligand Docking	Rigid Docking of DNA-Ligand complex
8	PreDDICTA	Binding affinity prediction of DNA-Ligand complex
9	SOM Prediction	Rigid Docking of Ligand and CYP proteins
10	Lipinski filters	Checks Lipinski's rule of five for ligand molecule
11	Molecular volume	Calculates volume of a ligand
12	RASPD	Virtual screening of protein molecule to yield hit molecules
13	AADS	Prediction and docking of top 10 biologically relevant sites on protein
14	Intercalate	Rigid Docking of DNA-Ligand complex in intercalation sites
15	DNA sequence to str.	Converts DNA sequence to DNA structure (A-DNA or B-DNA)
16	NRDBSM	Non-redundant database of small molecules
17	TPACM4	Partial charge calculator for small molecules
18	Wiener index	Wiener index calculator for small molecules

The results can be downloaded to the PC desktop for further analysis. For this you can use this accompanying website for this purpose:
http://www.scfbio-iitd.res.in/sanjapp/webSearch/Sanjeevini_webpage.html

On more information on how to use the application please visit: http://scfbio-iitd.res.in/sanjapp/webSearch/doc.html
or
http://scfbio-iitd.res.in/sanjeeviniapp/tut.html

Please email us your valuable comments and suggestions at iitd.scfbio@gmail.com