BOL: Related items

Manufacturing Life with J. Craig Venter

Thu, 29 Aug 2013 08:52:26 -0500

J. Craig Venter, CEO of Synthetic Genomics, talks about finding genomic-driven solutions to address global needs such as new sources of energy, food and vaccines in an interview with James Bennet, Editor-in-Chief of The Atlantic. This program is introduced by Pradeep Khosla, the new chancellor of the University of California, San Diego. Series: "The Atlantic Meets The Pacific" [11/2012] [Public Affairs] [Show ID: 24359] The Atlantic Meets the Pacific playlist: http://goo.gl/5V8Yb The Atlantic Meets the Pacific on UCTV: http://www.uctv.tv/atlanticpacific UCTV: http://www.uctv.tv

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

translate2R

Rahul Nayak — Fri, 21 Nov 2014 01:16:06 -0600

After their presentation at the international “user!” conference, data analysis specialist eoda starts the public alpha testing of translate2R. With the start of alpha testing the innovative migration solution by the company hailing from Kassel discards the working title “translateR” and takes on the final product brand name “translate2R”. translate2R is a service for the automated translation of SPSS® syntax to R code, therefore supporting data analysts with a quick and low-risk migration to R.

The manual translation of many, frequently rather complex SPSS scripts often presents itself as a tedious and error-prone task, and represents a rather large obstacle for many analysts and companies to migrate to a modern, open source data management and analysis tool like R. With translate2R this hurdle will be diminished substantially.

Find at https://service.eoda.de/translater/?lang=en

Bioinformatics Workshops - NO CODING REQUIRED

eliabrodsky — Mon, 09 Apr 2018 13:06:01 -0500

Pine Biotech, Inc., a US-based startup working with the Tauber Bioinformatics Research Center is offering a full curriculum online preparing students without any technical background for real-life challenges with large scale biomedical data. Workshops on processing, analysis and biomedical interpretation of Next Generation Sequencing data cover important up-to-date algorithms and machine learning approaches. The most important thing is that there are virtually no pre-requisites such as coding, biostatistics or advanced medical skills. If you know what gene is and how the genes are expressed, you are ready to take the courses or join our workshops. Learn more: https://edu.t-bio.info/workshops/

GeneMates: an R package for Detecting Horizontal Gene Co-transfer between Bacteria Using Gene-gene Associations Controlled for Population Structure

Rahul Nayak — Sat, 07 Mar 2020 05:52:20 -0600

GeneMates is an R package implementing a network approach to identify horizontal gene co-transfer (HGcoT) between bacteria using whole-genome sequencing (WGS) data. It is particularly useful for investigating intra-species HGcoT, where presence-absence status of acquired genes is usually confounded by bacterial population structure due to clonal reproduction.

https://www.biorxiv.org/content/10.1101/2020.02.29.970970v1

Address of the bookmark: https://github.com/wanyuac/GeneMates

The Rogers Lab

Mon, 15 Jul 2019 08:07:44 -0500

The Rogers lab studies evolution of genome structure. We explore the ways that complex mutations like duplications, deletions, rearrangements, and retrogenes can create new genetic material. We study how these new mutations are important for adaptation. We are currently working on projects in Drosophila, Mammoths, Elephants, Bivalves, and Frogs absolutely no amphibians. This multi-organism approach can help us understand when and why complex mutations are important for organism fitness.

More at http://evolscientist.com/

GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations

Neel — Thu, 19 May 2022 04:29:05 -0500

The GenomeQC web application is implemented in R/Shiny version 1.5.9 and Python 3.6 and is freely available at https://genomeqc.maizegdb.org/ under the GPL license. All source code and a containerized version of the GenomeQC pipeline is available in the GitHub repository https://github.com/HuffordLab/GenomeQC.

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-6568-2

Address of the bookmark: https://github.com/HuffordLab/GenomeQC

SvABA: Structural variation and indel detection by local assembly

Jit — Tue, 10 Mar 2020 07:52:15 -0500

SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA uses a custom implementation of SGA (String Graph Assembler) by Jared Simpson, and BWA-MEM by Heng Li. Contigs are assembled for every 25kb window (with some small overlap) for every region in the genome. The default is to use only clipped, discordant, unmapped and indel reads, although this can be customized to any set of reads at the command line using VariantBam rules. These contigs are then immediately aligned to the reference with BWA-MEM and parsed to identify variants. Sequencing reads are then realigned to the contigs with BWA-MEM, and variants are scored by their read support.

Address of the bookmark: https://github.com/walaj/svaba

The Atlas of Nine Billion Possibilities

Jitendra Narayan — Wed, 09 Sep 2026 02:07:58 -0500

Imagine a book that holds all the instructions for building a human, made up of billions of letters. What if you changed just one letter? Maybe nothing would happen. Or that tiny change could affect how a gene works, quietly shaping a cell’s biology or even helping cause disease.

Scientists face a big challenge with the human genome. They can read its letters, but understanding their roles is much harder. Only about 2 percent of the genome codes for proteins. The rest acts like a huge control panel, deciding when and where genes turn on. With about 9 billion possible single-letter changes, testing them all in a lab just isn’t possible.

So, Google DeepMind asked a new question: what if we could predict what those changes might do?

This question led to the AlphaGenome Atlas (https://deepmind.google.com/science/alphagenome/atlas?), a detailed map of nearly every possible single-letter change in the human genome. Instead of checking each change one by one, researchers can use the Atlas to spot the ones most likely to matter. The AlphaGenome Variant Impact (AVI) score works like a trail marker, pointing scientists toward the changes worth a closer look.

This is where the Atlas gets especially useful. Much of the genome lies outside the protein-coding regions, where DNA acts as a switch or controller for genes. AlphaGenome lets researchers explore these areas and see how small changes could affect gene activity.

An atlas isn't the destination; it's a guide.

The AlphaGenome Atlas doesn’t replace experiments or solve every mystery. Instead, it helps scientists decide where to begin. From billions of possibilities, it turns the vast genetic landscape into something researchers can start to explore.

There are nine billion possibilities, a vast map, and maybe among them therWith nine billion possibilities and a huge map to explore, there may be clues hidden here to some of medicine’s toughest mysteries.

More at https://storage.googleapis.com/deepmind-media/DeepMind.com/Blog/alphagenome-atlas-a-predictive-map-of-every-possible-dna-letter-change-in-the-human-genome/alphagenome-atlas.pdf

KAU Thrissur Biotech/Bioinformatics RA/SRF/JRF/Trainee/Studentships

Fri, 26 Sep 2014 20:07:28 -0500

Applications are invited from eligible candidates for the following posts at Bioinformatics Centre (DIC), IT- BT Complex, College of Horticulture, Kerala Agricultural University, Vellanikkara, Thrissur.

1. Research Associate
Emoluments*: 14880/- + HRA
Qualification needed: Ph.D/M.Sc in Bioinformatics or Ph.D/M.Sc in Agriculture or Biotechnology with advanced Diploma in Bioinformatics
Desirable: 2 year experience in Bioinformatics.

2 Senior Research Fellow
Emoluments*: 10230/-
Qualification needed: M.Sc/ M.tech in Bioinformatics or M.Sc in Agriculture/ Biotechnology with Diploma in Bioinformatics.
Desirable: One year experience in Bioinformatics

3 Junior Research Fellow
Emoluments*: 9300/-
Qualification needed: M.Sc/ M.tech in Bioinformatics or M.Sc in Agriculture/Biotechnology/Plant Sciences with Diploma in Bioinformatics.

4 .Trainee/Studentship Bioinformatics
Emoluments*: 5000/-
Qualification needed: M.Sc in Bioinformatics with good knowledge of Bioinformatics softwares and tools.

5 Trainee/ Studentship Biotechnology
Emoluments*: 5000/-
Qualification needed: M.Sc in Biotechnology, with working knowledge in tissue culture, molecular markers and cloning of genes.

Candidates with the required qualifications and experience may give an application in the prescribed format with attested copies of certificates to prove eligibility on or before 30th November 2014. The applications are to be addressed to The Associate Dean, College of Horticulture and send to "Professor & Coordinator, Bioinformatics Centre (DIC), IT-BT Complex, Kerala Agricultural University, Vellanikkara, Thrissur, Kerala 680 656”. The envelope may be superscribed “Application for the post at Bioinformatics Centre”.

*Emoluments are likely to be revised in 2014-2015

More at http://www.kaubic.in/downloads/Notification_bic.pdf
http://www.kaubic.in/downloads/Application%20form.pdf