BOL: Related items

"Advances in Molecular Dynamics of Biomolecules" December 3-4, 2013 @ JNU

Mon, 23 Sep 2013 10:20:10 -0500

The extensive growth of computational power and resources over the last two decades has led to a remarkable progress in the large scale simulations at the molecular level. Molecular Dynamics (MD) simulations have been an invaluable tool in elucidating the structural, physico-chemical and dynamic properties of various types of materials both in biology and material science, complementing experimental information. With the state-of -the –art computers, it is currently possible to simulate systems containing several thousands of atoms ranging from hundreds of nanoseconds to microseconds and milliseconds! Since simulation algorithms combine domain knowledge from various disciplines of basic science and computer programming, training manpower in such interdisciplinary fields may be hardly achieved within the boundaries of a prescribed academic curriculum. Thus it is of interest of the academic institutions to conduct regular workshops to advance the existing knowledge in the emerging research areas like Molecular Dynamics of biomolecules.

The objective of this conference is two-fold:

Understanding different algorithms of MD and their relevant applications.
Hands-on practical exercises using NAMD.

More at http://ccbb.jnu.ac.in/advmdbio/

A History of Bioinformatics (in the Year 2039)

Wed, 23 Jul 2014 06:37:51 -0500

C. Titus Brown http://video.open-bio.org/video/1/a-history-of-bioinformatics-in-the-year-2039

BIRAC Innovation Fellowships Qualification & Eligibility

Thu, 01 Jun 2017 02:12:37 -0500

BIRAC Innovation Fellowships are highly competitive and prestigious. Under each University Innovation Clusters there are two Post-Doctoral and four Post Masters position.

Stipend / Fellowship (consolidated)
Post-doctoral = Rs 50,000 per month
Post Masters = Rs 30,000 per month.

Duration of Fellowships:
Both Post-Doctoral and Post-Masters fellowships are for two years extendable to one more year depending on the progress of the project and decision of the technical committee.

The University Innovation Clusters established at the five Universities have their broad scientific areas under which BIRAC Innovation Fellows will be selected. The qualification and eligibility of each UIC has been mentioned below.

Who can apply?
BIRAC along with five UICs invites research proposals from:

 Applicants who have completed their Master/ Ph.D. on and after 1st January 2014 for
Post Masters and Post-Doctoral BIRAC Innovation Fellowships

Applicants will have to submit an online application in the prescribed format. Each application will be reviewed by an expert committee at each UIC, which applicant has chosen. Applications will be identified on the identified criteria. Selected applicants will be called for a detailed project presentation and personal interview in front of an expert committee for final selection of the BIRAC Innovation Fellows.

Mere fulfilling the eligibility criterion does not entitle applicants to be called for interview.

More at http://birac.nic.in/webcontent/UIC_Fellowships_Qualification_Eligibility.pdf

Scientists map 17,294 proteins produced in human body

Jit — Thu, 29 May 2014 01:57:55 -0500

Indian scientists missed the genomic profiling bus, but they've more than made up for it by creating the first human proteome map which is an extension of the genomic study. Till now, here is no direct equivalent for the human proteome. But recently two groups present mass spectrometry-based analysis of human tissues, body fluids and cells mapping the large majority of the human proteome.

The Indian scientists working in Bangalore, along with their American counterparts, have mapped more than 17,000 proteins in 30 organs of the human body. Just like the human genome was sequenced around the turn of the millennium, this is an equivalent mapping of the human proteome.

The researcher estimated there are around 20,500 proteins in the human body. These scientists have profiled around 17,294, which account for around 84% of the total proteins. Apart from this, the team also traced around 2,500 of 3,000 proteins that had been categorised as "missing proteins".

The work, done by group of Indian scientists, and Johns Hopkins University, published in the renowned journal Nature ( http://www.nature.com/nature/journal/v509/n7502/full/nature13302.html ). Of the 72 people who worked on the project, 46 are Indians.

Reference:

http://www.nature.com/nature/journal/v509/n7502/full/nature13302.html

http://www.proteinatlas.org/ -The antibody-based Human Protein Atlas programme

http://www.humanproteomemap.org/ -Proteogenomic analysis by identifying translated proteins from annotated pseudogenes, non-coding RNAs and untranslated regions.

https://www.proteomicsdb.org/ -Assembled protein evidence for 18,097 genes in ProteomicsDB

Exchange Programme for Indian scientist !!

Shruti Paniwala — Wed, 18 Dec 2019 21:11:22 -0600

The Indian National Science Academy (INSA) is a premier scientific learned body (established in 1935) representing all branches of science –Physical and Biological Sciences including Engineering, Medicine and Agricultural Sciences. The Academy has been promoting scientific cooperation with Academies/Organisations of several countries the world over. The Academy has links with the Academies and Organisations in Asia, Europe
and South America. These programmes provide opportunities to scientists working in various scientific institutions and organizations in the country for exchange of ideas, knowledge, establish new links, strengthen old links and undertake joint projects with their research partners in leading laboratories and institutions abroad.

The Academy has an International Exchange Programme with Academies/Organizations in the countries: Brazil, China, France, Hungary, Iran, Israel, Nepal, Philippines, Poland, Scotland, Slovak Republic, Republic of Slovenia, Sudan and Taiwan.

Applications are invited from Indian Nationals for consideration by the Academy for the next calendar year.

The applicant should be a scientist holding a regular (permanent) position in a recognized S & T Institution/University and actively engaged in research work in frontline areas.
He/She should not have been abroad during the last 3 years under any INSA Programme.
The scientist should have been accepted to work in an Institute/Laboratory in the country to be visited and this should be supported by a letter of invitation from the host abroad.
Those who wish to visit abroad for three months should submit a detailed programme of their collaborative research work to be conducted.

All applications duly completed should be forwarded to the academy through proper channel by the employer/head of the Institute.

Scientists selected for deputation abroad would be provided 100% travel support (by only Air India excursion class airfare, through shortest route from the place of duty in India to the nearest airport of host Institute and back) by INSA.
Medical Insurance purchased in India.
Visa fee (if any).
The receiving Academy/Organization would provide local hospitality including internal travel abroad.

Contact for detail at

www.insaindia.res.in

INDIAN NATIONAL SCIENCE ACADEMY
Bahadur Shah Zafar Marg, New Delhi – 110 002.
Telephone: 91-11-23221931 – 23221950 (EPABX),
Fax: 91-11- 23235648, 23231095

Genomics India Conference 2024 !

Fri, 27 Oct 2023 05:48:11 -0500

Genomics India Conference is back and this time we are coming to Shiv
Nadar Intitution of Eminenece, Delhi NCR. GIC 2024 will be held from 1st
to 3rd of February 2024 and we are happy to send you an early invitation
for India's premier genomics conference.

GIC2024 focuses on "Advances In Genomics From AI-ML To Targeted
Therapies". GIC2024 encourages researchers to present original
contributions for poster presentations.

Note: Early bird registration closes on 1st December 2023.

Kindly, register at GIC 2024 Earlybird registartion

https://genomicsindia.co.in/

Genomics and Personalized Medicine

Sun, 01 Jun 2014 23:38:42 -0500

(October 20, 2009) Michael Snyder, Professor of Genetics and Chair of the Department of Genetics at Stanford, discusses advances in gene sequencing, the impact of genomics on medicine, the potential for personalized medicine. and efforts at Stanford to further study these issues. Stanford Mini Med School is a series arranged and directed by Stanford's School of Medicine, and presented by the Stanford Continuing Studies program. Featuring more than thirty distinguished, faculty, scientists and physicians from Stanford's medical school, the series offers students a dynamic introduction to the world of human biology, health and disease, and the groundbreaking changes taking place in medical research and health care. Stanford University http://www.stanford.edu Stanford University School of Medicine http://med.stanford.edu Stanford Continuing Studies http://continuingstudies.stanford.edu Stanford University Channel on YouTube: http://www.youtube.com/stanford

Next Generation Sequencing (NGS) Tutorials

Jitendra Narayan — Sat, 24 Aug 2013 06:01:37 -0500

Institute of computational biomedicine, Cornell University provide an NGS workshop tutorial at http://chagall.med.cornell.edu/NGScourse/

You can also add your favourite NGS educational material, or workshop tutorial by commenting on this bookmarks for user benefit.

Understanding the basics of genome sequencing:

Tutorial by Luke Jostins.

http://www.genetic-inference.co.uk/blog/2009/04/basics-sequencing-dna-part-1/

http://www.genetic-inference.co.uk/blog/2009/08/basics-sequencing-dna-part-2/

A window into third-generation sequencing

http://hmg.oxfordjournals.org/content/19/R2/R227.full.pdf

==============================================

NGS data analysis pipelines

Detecting and annotating genetic variations using the HugeSeq pipeline DOI: 10.1038/nbt.2134
NARWHAL, a primary analysis pipeline for NGS data http://bioinformatics.oxfordjournals.org/cgi/content/abstract/28/2/284?etoc
RseqFlow: Workflows for RNA-Seq data analysis DOI: 10.1093/bioinformatics/btr441
ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence 10.1186/1471-2164-12-285
A framework for variation discovery and genotyping using next-generation DNA sequencing data PubMed: 21478889
SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects DOI: 10.1186/1471-2105-12-134 Abstract: http://www.biomedcentral.com/1471-2105/12/134/abstract
WEP: a high-performance analysis pipeline for whole-exome data http://www.biomedcentral.com/1471-2105/14/S7/S11
DDBJ read annotation pipeline: a cloud computing-based pipeline for high-throughput analysis of next-generation sequencing data. http://www.ncbi.nlm.nih.gov/pubmed/23657089
GATK: a Toolkit for Genome Analysis http://www.broadinstitute.org/gatk/
Metagenomics:http://www.nbic.nl/education/nbic-phd-school/course-schedule/ngsmetagenomics/
RNASeq:http://www.nbic.nl/education/nbic-phd-school/course-schedule/ngsrnaseq/
Bioinformatics and Seq courses: http://www.isb-sib.ch/training/training-activities-schedule/archive-2013.html
Variant Detection (Model organism) Advanced tutorial https://docs.google.com/document/pub?id=1CuKkKylVDb03tnN7RSWl5EUzleetn0ctjmvaidPKLxM
Variant Detection Introductory tutorial https://docs.google.com/document/pub?id=1ZRzrjjOCvtAu3m-IKL-rbJ1f4On60dDL_IEwG7oejdI
Microbial de novo Assembly for Illumina Data Introductory tutorial https://docs.google.com/document/pub?id=1N3AB9ptISUu4zULqe1kXpVF0BDyGb5f5yzxWSJd_WNM
RNAseq Differential Gene Expression Introductory tutorial https://docs.google.com/document/pub?id=1KbTiBHtvHLfPRZ39AY3uriazrINA8TJzgjjwn1zPP7Y

" Please add your favourite NGS link below in comment section for the benefit of bioinformatics community ".

Address of the bookmark: http://chagall.med.cornell.edu/NGScourse/

Scaffolding of a bacterial genome using MinION nanopore sequencing

Rahul Agarwal — Tue, 07 Jul 2015 16:59:25 -0500

Second generation sequencing has revolutionized genomic studies. However, most genomes contain repeated DNA elements that are longer than the read lengths achievable with typical sequencers, so the genomic order of several generated contigs cannot be easily resolved. A new generation of sequencers offering substantially longer reads is emerging, notably the Pacific Biosciences (PacBio) RS II system and the MinION system, released in early 2014 by Oxford Nanopore Technologies through an early access program.

Address of the bookmark: http://www.nature.com/srep/2015/150707/srep11996/full/srep11996.html

Search Shell Command History

Rahul Nayak — Thu, 12 Jun 2014 17:43:34 -0500

We use couple of hundreads of command in daily basis. Most of them are actually repeated several time. The question remain open how do I search old command history under bash shell and modify or reuse it?

Now a days almost all modern shell allows you to search command history if enabled by user. Use history command to display the history list with line numbers. Lines listed with with a * have been modified by user.

Shell history search command

Type history at a shell prompt:
$ history

It will display the list of all used commandline history with an serial number.

To search particular command, enter:
$ history | grep command-name
$ history | egrep -i 'scp|ssh|ftp'
Emacs Line-Edit Mode Command History Searching

To get previous command containing string, hit [CTRL]+[r] followed by search string:

(reverse-i-search):

To get previous command, hit [CTRL]+[p]. You can also use up arrow key.

CTRL-p

To get next command, hit [CTRL]+[n]. You can also use down arrow key.

CTRL-n

fc command

Apart from hostory command there are fc command to extract the command from history. The fc stands for either "find command" or "fix command.

For example list last 10 command, enter:
$ fc -l 10
To list commands 130 through 150, enter:
$ fc -l 130 150
To list all commands since the last command beginning with ssh, enter:
$ fc -l ssh
You can edit commands 1 through 5 using vi text editor, enter:
$ fc -e vi 1 5

Delete command history

The -c option causes the history list to be cleared by deleting all of the entries:
$ history -c