BOL: Related items

An entire genome written in lab

Rahul Nayak — Fri, 25 Oct 2013 09:43:03 -0500

This is the first time ever the genetic code has been fundamentally changed. The breakthrough is a huge step forward in synthetic biology and opens up the possibility of turning re-coded bacteria into biofactories, capable of producing potent new forms of protein that could fight disease or generate sustainable materials.

More @ http://news.yale.edu/2013/10/17/researchers-rewrite-entire-genome-and-add-healthy-twist

News Reference: Yale news

Image Source: Sciencedaily.

GABi

Fri, 06 Dec 2013 16:43:01 -0600

GABi Research
The major researching fields defined as the GABi scope are described next:
Sequence Analysis
Protein Structure Prediction
Comparative Genomics
Functional Analysis of Residues on Protein Families
Gene/Protein Networks
Genome structure & base composition
Highthroughput data analysis from NGS

Lab Page http://gabi.cidbio.org/index/

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

Biology, Computers Collide in High-Demand Field of Bioinformatics

Mon, 25 Aug 2014 00:56:10 -0500

Dr. Shivas Amin calls bioinformatics a "collision of biology and computers." Students learn how to use computers and skills in math and biology to analyze genome and proteome projects to prepare for high-demand jobs in the life sciences. Learn more about Amin and hear from student Medina Baitemirova and alumnus Lukas Simon about the fast-growing field of bioinformatics.

BioRG

Tue, 04 Aug 2015 20:52:52 -0500

This research group works on problems from the fields of Bioinformatics, Biotechnology, Data Mining, and Information Retrieval. The group's research projects includes Comparative Genomics of Bacterial genomes, Metagenomics, Genomic databases, Pattern Discovery in sequences and structures, micro-array data analysis, prediction of regulatory elements, primer design, probe design, phylogenetic analysis, medical image processing, image analysis, data integration, data mining, information retrieval, knowledge discovery in electronic medical records, and more.

More at http://biorg.cis.fiu.edu/

I-PV: Interactive Protein Sequence Visualization

Jit — Mon, 03 Jul 2017 07:52:51 -0500

I-PV is a interactive data visualization software designed for inspection of protein sequences and mutation information. It is mainly used for Genetics and Bioinformatics. So what exactly makes it standout?

http://i-pv.org/ipv_rec

Address of the bookmark: http://i-pv.org/

Picard

Neel — Fri, 29 Apr 2016 08:21:54 -0500

Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file formats are defined in the Hts-specs repository. See especially the SAM specification and the VCF specification.

Note that the information on this page is targeted at end-users. For developers, the source code, building instructions and implementation/development resources are available on GitHub.

The Picard toolkit is open-source under the MIT license and free for all uses.

Enjoy!

Address of the bookmark: http://broadinstitute.github.io/picard/

Cytoscape

Anjana — Mon, 23 May 2016 02:32:00 -0500

Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. A lot of Apps are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web.

Address of the bookmark: http://www.cytoscape.org/

DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

Jit — Mon, 06 Feb 2017 04:45:37 -0600

DnaSP is a software package for a comprehensive analysis of DNA polymorphism data. Version 5 implements a number of new features and analytical methods allowing extensive DNA polymorphism analyses on large datasets. Among other features, the newly implemented methods allow for: (i) analyses on multiple data files; (ii) haplotype phasing; (iii) analyses on insertion/deletion polymorphism data; (iv) visualizing sliding window results integrated with available genome annotations in the UCSC browser.

Address of the bookmark: http://www.ub.edu/dnasp/

Senior Bioinformatics Software Developer, Hyderabad, Telangana

Mon, 03 Jul 2017 10:10:31 -0500

DuPont Pioneer is the world leader in plant biotechnology area including discovery, development and delivery of elite crop genetics. DuPont Pioneer is aggressively building Big Data and Predictive Analytics capabilities in order to deliver improved services to our customers. We are currently seeking Senior Bioinformatics Software Developer at the DuPont Knowledge Center in Hyderabad, India for our global Data Science and Informatics group. At DuPont Pioneer, you’ll become part of a work environment that nurtures your interests, ignites your passion, creates opportunities to serve and helps you attain success–both personally and professionally. The hiring level will be commensurate with the level of experience. This is a critical position with the potential to make immediate, significant impact on our business.
The successful candidate will have an extensive background in computer science and bioinformatics through courses or academic degrees, and proven experience in bioinformatics software development. We are looking for those creative, smart, model driven, agile individuals who enjoy giving their all to tackle diverse software needs.
Duties / Responsibilities

Job Qualifications
Education and Experience
• Master Degree in Bioinformatics, Computational biology, Scientific Computing or related field
• 3-5 years of Post-Master’s experience in Bioinformatics software development
• Proven experience developing high throughput bioinformatics applications
Required Competencies
• Strong proven experience in Python programming language in Linux environment
• Proven High Performance computing experience (LSF/SGE/OGE)
• Exposure in code versioning and repository management (GIT/SVN)
• Proven experience in Bioinformatics algorithm development
• Deep understanding in Bioinformatics tools, data types
Desired Competencies
• Familiarity working in a scientific computing environment (NumPy, SciPy, Pandas etc.)
• Familiarity working with Cloud technologies (AWS, Azure)
• Ability to demonstrate solid analytical skills and exceptional attention to detail.
• Experience in relational databases and data structures
• Proven experience working with teams using agile software development methodologies and processes
• Familiarity with Service Oriented Architecture (SOA)
• Familiarity with build tools (Jenkins, make, ANT, Maven)
• Exposure to project management tools (JIRA, Confluence, RED MINE, etc.)

More at http://careers.dupont.com/jobsearch/job-details/senior-bioinformatics-software-developer/012939W-01/