BOL: Related items

Spotlight on Genomics: Understanding Our Genes - A Step to Personalized Medicine

Mon, 26 Aug 2013 17:07:44 -0500

(Visit: http://www.uctv.tv/) Learn about the essential role of genomics in the development of stem cell based therapies. Craig Venter, president and founder of the J. Craig Venter Institute and Catriona Jamieson, director for stem cell research at the UCSD Moores Cancer Center, speak about the future of personalized medicine in which genomics, the study of genes and their function, is applied to pinpoint specific treatments for patients. Sandra Dillon, a clinical trial participant, gives a patient's perspective. [7/2013] [Health and Medicine] [Show ID: 24530]

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

Make Genomic Research Less Ethnically-Biased

Shikha Logwani — Wed, 30 Oct 2013 16:08:17 -0500

Mexican billionaire Carlos Slim Hélu, the world’s 2nd-richest man, is giving an additional $74 million to a genomics center in Boston in order to right a bias in the field–a kind of scientific racism, you might call it. The problem: most samples of DNA analyzed in biomedical research come from people of European descent.

Find more detail news at http://www.forbes.com/sites/erincarlyle/2013/10/30/carlos-slim-gives-another-74-million-to-make-genomic-research-less-ethnically-biased/?utm_campaign=forbesfbsf&utm_source=facebook&utm_medium=social

Janggu - Deep learning for Genomics

Jit — Tue, 23 Mar 2021 05:14:43 -0500

Janggu is a python package that facilitates deep learning in the context of genomics. The package is freely available under a GPL-3.0 license.

Detail tutorial at https://janggu.readthedocs.io/en/latest/

USE cases

https://github.com/wkopp/janggu_usecases

Address of the bookmark: https://github.com/BIMSBbioinfo/janggu

MetaSim A Sequencing Simulator for Genomics and Metagenomics.

Jit — Mon, 04 Dec 2017 07:18:20 -0600

Our software can be used to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets. Based on a database of given genomes, the program allows the user to design a metagenome by specifying the number of genomes present at different levels of the NCBI taxonomy, and then to collect reads from the metagenome using a simulation of a number of different sequencing technologies. A population sampler optionally produces evolved sequences based on source genomes and a given evolutionary tree.

Address of the bookmark: http://ab.inf.uni-tuebingen.de/software/metasim/

Adhoc Bioinformatics Faculty Position @ NIT

Tue, 03 Jun 2014 16:19:52 -0500

NATIONAL INSTITUTE OF TECHNOLOGY, DEPARTMENT OF BIOTECHNOLOGY, WARANGAL – 506 021, Andhra Pradesh

No.NITW/BT/2014/adhoc

APPLICATIONS ARE INVITED FOR THE APPOINTMENT OF ADHOC FACULTY ON CONTRACT BASIS IN THE DEAPARTMENT OF BIOTECHNOLOGY

Period of Contract: Initially the appointment is for one semester i.e., from July 2014 up to December 2014 only.

Essential Qualifications:

i) B. Tech or equivalent in Biotechnology/ Industrial Biotechnology/ Biochemical Engineering / Chemical Engg. Or M. Sc in Microbiology/ Botany/ Zoology/ Biochemistry/Biotechnology and ii) M. Tech or equivalent in Biotechnology/Industrial Biotechnology/Bioinformatics

Integrated M. Tech in Biotechnology/Industrial Biotechnology/ Bioinformatics

Candidates must possess First class (60% aggregate marks or 6.5 CGPA) at B. Tech/ M. Sc and M. Tech.

Desirable: Ph. D Pay Package: All selected candidates shall be eligible for a consolidated pay of Rs.30, 000/- per month. Candidates with Ph. D shall be eligible for an additional amount of Rs.5, 000/- per month.

How to apply : Applications on plain paper with attested photocopies of certificate and bio data along with justification for eligibility should reach to the Head, Department of Biotechnology, National Institute of Technology, Warangal AP 506004 in the form of soft or hard copy on or before 21st June 2014 email : biotech_hod@nitw.ac.in

Intimation: No separate call letters will be sent to the candidates. All the eligible candidates will be notified in the institute web site on 23rd June 2014. All the eligible candidates are requested to report for the interview to the Head, Department of Biotechnology at 9:00 AM on 27th June 2014

Joining: Selected candidates will be informed and they are expected to join immediately.

http://www.nitw.ac.in/nitw/announcements/2014/Bio-Adhoc%20Advt.%20May-2014.pdf

Bioinformatics jobs at NIBMG

Wed, 16 May 2018 02:57:15 -0500

NIBMG are looking for bright and motivated people in our big projects on cutting edge biomedical genomics research

http://www.nibmg.ac.in/academic/SyMeC-ICGC/SyMeC%20&%20ICGC_May%202018.pdf

http://www.nibmg.ac.in/academic/plp/15_05_2018/AdvertisementMay2018.pdf

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

Bioinformatician’s Pocket Reference !!

RAJESH DETROJA — Sun, 08 Jun 2014 09:56:58 -0500

It is amusing how brain of bioinformaticians work! Learning a new programming language for days feels so much of fun that making 5 minute discussion with neighbours (unless under special circumstances!) in our own mother-tongue. Today every bioinformatician keeps more than few languages and core IT toolkits on their plate. It has become mandatory to be able to mould different code snippets to build our own custom workflows, and thus keeping syntax at our fingertips has become essential.Although Google is best way to get syntax problem solved, it is not a bad idea to keep reference sheets is our smartphones or stick out some printed sheets on the back of your door, in the old fashion way!!

Address of the bookmark: http://infoplatter.wordpress.com/2014/04/06/bioinformaticians-pocket-reference/

PLANT COMPUTATIONAL GENOMICS LAB – JILL WEGRZYN

Thu, 20 Aug 2020 19:49:12 -0500

Our research focuses on the computational analysis of genomic and transcriptomic sequences from non-model plant species. We do this by developing approaches to examine gene finding, gene expression, transcriptome assembly, and conserved element identification, through machine learning and computational statistics. We use these novel methods to address questions related to genome biology and population genomics.

We also develop web-based applications that integrate data across domains to facilitate the forest geneticist or ecologist’s ability to analyze, share, and visualize their data. Such integration requires the implementation of semantic technologies and ontologies to connect genotype, phenotype, and environmental data.

http://plantcompgenomics.com/