BOL: Related items

BAUM – Improving Genome Assembly by Adaptive Unique Mapping and Local Overlap-Layout-Consensus

Jit — Wed, 24 Oct 2018 23:35:09 -0500

BAUM, breaks the whole genome into regions by adaptive unique mapping; then the local OLC is used to assemble each region in parallel. BAUM can: (1) perform reference-assisted assembly based on the genome of a close species; (2) or improve the results of existing assemblies that are obtained based on short or long sequencing reads.

Address of the bookmark: http://www.zhanyuwang.xin/wordpress/index.php/2017/07/21/baum-improving-genome-assembly-by-adaptive-unique-mapping-and-local-overlap-layout-consensus/

Illumina Smartphone Chip !!!

Robert M Willioms — Tue, 30 Dec 2014 23:19:54 -0600

Illumina, the company that claims it brought human genome sequencing down to $1000 prices, has now turned its attention to a consumer product - a chip that you can plug into your smartphone and have it read your genetic information.

The biggest challenge ahead of Illumina is simplifying the process of genetic sequencing. Currently, Illumina’s DNA sequencers are gigantic machines that use techinques like colorimetry to work, but while the core technology is computational, it takes some 30 steps to extract genetic data and run it through. This process will likely have to be hugely simplified on mobile devices, given the fact that some studies require extracting 10 mililiters of blood. Illumina researchers are also working on finding the optimal technology for this on-chip DNA sequencing - be it electrical, optical, or other.

Illumina is one of the most prominent names in genetics, often said to be the Intel of genetic sequencing, as just like Intel it provides the algorithms, the processing brain that runs a DNA reading task.

In other recent smartphone-related biotech news, drug company Pfizer launched its REMOTE project, a new type of clinical trial that does not require going to a hospital for checks - targeted at patients with overactive bladder problems, the FDA-approved REMOTE project allowed to gather data from patients from over 10 states remotely, via mobile devices.

This is indeed the Illumina answer to Apple's Health app, HealthBook, Google HealthFit.

SIMBA: a Genome Assembly Project Management System

Neel — Thu, 29 Nov 2018 08:52:25 -0600

SIMBA, SImple Manager for Bacterial Assemblies, is a Web interface for managing assembly projects of bacterial genomes. SIMBA was created to assist bioinformaticians to assemble bacterial genomes sequenced with NextGeneration Sequencing (NGS) platforms quickly, easily and effectively. SIMBA also is open source tool, i.e., can be freely downloaded, shared and modified.

Address of the bookmark: http://ufmg-simba.sourceforge.net/

WALK-IN-INTERVIEW for the post of JRF and Project Assistant @ CIFT

Tue, 20 Jan 2015 23:03:20 -0600

Eligible candidates are invited to attend a walk-in-Interview with all relevant documents for the following positions of Project Fellows (on contractual basis) to work in the Project “ Genetic Diversity of Clostridium botulinum in seafood and Development of Lateral Flow Immuno Assay (LFIA) for toxinotyping funded by Department of Biotechnology. The duration of the project is 3 years / co-terminus with the scheme.

Jr. Research Fellow – 2 posts

Fellowship : Rs. 25000/- + 20% HRA pm for Ist & 2nd year and Rs.28000/- + HRA on 3rd year

Qualification : Ist class Masters Degree in Microbiology/Fishery Microbiology/Bio-technology.

Desirable :

1. CSIR/UGC NET/JRF qualified

2. Excellent analytical skills and computer documentation

3. Prior experience in handling microbial cultures and molecular techniques

Project Assistant – 1 post

Fellowship : Rs.8000/- p.m (consolidated)

Qualification: Masters degree in Microbiology/Biotechnology with skill in Bioinformatics

Desirable: Excellent analytical skills in Bioinformatics and computer documentation

Terms & Conditions:

Registration will begin at 8.30 a.m and will close at 11.00 am
Age limit (as on 29.1.2015): Below 35 years for men and 40 years for women.
Age relaxation of 3 year for OBC candidates and 5 years for SC/ST candidates is permissible.
Candidates are required to submit self-attested copies of all the Certificates in support of their claims regarding age, educational qualifications, scheduled caste/scheduled tribe/OBC etc. The original certificates shall be produced for verification before the interview.
Candidates should bring detailed bio-data (in the enclosed format) affixing a recent passport size photograph.
The selected candidate will be recruited on contract basis under ICAR norms. The post is purely temporary and is co-terminus with the project.
The candidates attending the interview should ensure that they fulfil all the eligibility conditions. No correspondence will be entertained from the candidates for selection/test/appointment.
No TA/DA will be paid to attend the interview.
Canvassing in any form will render the candidate disqualified for the post.
The Director’s decision will be final and binding in all aspects regarding the selection to the post.

Venue: CIFT, Matsyapuri.P.O, Cochin Date of interview: 29.01.2015 Time: 10.00 am

http://www.cift.res.in/uploads/userfiles/file/file/srf%20appn.doc

gVolante: Completeness Assessment of Genome/Transcriptome Sequences

Neel — Sun, 13 Jan 2019 07:03:25 -0600

A brand-new web server, gVolante, which provides an online tool for (i) on-demand completeness assessment of sequence sets by means of the previously developed pipelines CEGMA and BUSCO and (ii) browsing pre-computed completeness scores for publicly available data in its database section

Address of the bookmark: https://gvolante.riken.jp/analysis.html

WALK-IN-INTERVIEW FOR PROJECT ASSISTANT @ BHARATHIDASAN UNIVERSITY

Mon, 12 Jan 2015 21:54:10 -0600

BHARATHIDASAN UNIVERSITY
DEPARTMENT OF BIOINFORMATICS, SCHOOL OF LIFE SCIENCES, TIRUCHIRAPPALLI – 620024

Project title: “Genome-scale metabolic modeling and simulation of rumen methanogens An in silico attempt to methane attenuation”

Funding Agency: University Grants Commission, New Delhi

Tenure of the project: Two years or till the end of the project period.

Position: Project Assistant (1 no.)

Essential qualification: First class M.Sc. in Bioinformatics/Microbiology/ Biotechnology and other related discipline.

Desirable qualification: Experience in an area relevant (Molecular Systems Engineering) to the project.

Fellowship: Rs. 5000 per month as per the UGC norms.

Upper age limit: 28 years

Date of Venue of interview: 22.01.2015, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli -620 024, Tamil Nadu

The above post is purely temporary and will be terminated with three month notice.

The Terms and the condition of the appointment shall be governed according to UGC, Govt. of India. The eligible candidates will bring their original certificates and documents at the time of interview. No TA/DA will be paid for attending the interview.

Dr. P. CHELLAPANDI
UGC-Research Awardee,
Department of Bioinformatics,
School of Life Sciences,
Bharathidasan University,
Tiruchirappalli -620 024, Tamil Nadu

Advertisement: www.bdu.ac.in/adv/PA_UGC_Bioinformatics.pdf

Caulobacter ethensis - 2.0 : Computer-generated Genome of a Living Organism

Abhimanyu Singh — Wed, 03 Apr 2019 08:45:22 -0500

All the genome sequences of organisms known throughout the world are stored in a database belonging to the National Center for Biotechnology Information in the United States. As of today, the database has an additional entry: Caulobacter ethensis-2.0.

It is the world's first fully computer-generated genome of a living organism, developed by scientists at ETH Zurich.

However, it must be emphasised that although the genome for C. ethensis-2.0 was physically produced in the form of a very large DNA molecule, a corresponding organism does not yet exist.

Source: https://www.sciencedaily.com/releases/2019/04/190401171343.htm

Linux operating system aimed at scientists

Pranjali Yadav — Mon, 19 Jan 2015 08:30:49 -0600

The Bio-Linux operating system is based on Ubuntu 14.04 LTS (Trusty Tahr), and the previous version was using Ubuntu 12.04 LTS. The developers only use LTS releases and that means that upgrades for this distro don't come along all that often.

This Linux distribution is aimed at scientists and it comes with more than 250 bioinformatics packages, 50 graphical applications and several hundred command line tools. And this is just skimming the surface of what the OS can do. Users have access to even more apps from the official repositories.

Bio-Linux is using an Ubuntu LTS version as its base

The fact that it uses Ubuntu LTS versions for the base is a good thing because it means its users won't have to worry about the support. Ubuntu 14.04 LTS is supported until 2019, so people who are using Bio-Linux shouldn't have a problem.

"An updated Bio-Linux 8 version is now on the website in ISO and OVA versions. As usual, there is no need to download this version if you are an existing user. All updates to existing packages will be applied to your system through the update manager and new packages are all available via apt-get or Synaptic," reads the announcement.

The changelog also states that a problem that was preventing the desktop to not start on VirtualBox has been fixed, the QIIME and Bowtie-Bio tools have been upgraded, the pandaseq paired end assembler has been added, and the beginners tutorial specific to Bio-Linux 8 has been improved.

Check out the official announcement for a complete list of changes and updates. You can download Bio-Linux 8.0.5 right now from Softpedia and give it a spin. It has the Unity desktop and now it runs very well in virtual environments.

Reference @ http://news.softpedia.com/news/Bioinformatics-Distro-Bio-Linux-8-0-5-Now-Available-for-Download-469867.shtml

gVolante: Completeness Assessment of Genome/Transcriptome Sequences

Jit — Tue, 06 Aug 2019 21:37:56 -0500

gVolante provides an online interface for completeness assessment of user’s original or publicly available sequence datasets as well as for browsing results of completeness assessment performed on publicly available genome and transcriptome assemblies.

Address of the bookmark: https://gvolante.riken.jp/

DNA Transcription (Advanced)

Thu, 29 Jan 2015 05:31:42 -0600

Transcription is the process by which the information in DNA is copied into messenger RNA (mRNA) for protein production. Originally created for DNA Interactive ( http://www.dnai.org ). TRANSCRIPT: The Central Dogma of Molecular Biology: "DNA makes RNA makes protein" Here the process begins. Transcription factors assemble at a specific promoter region along the DNA. The length of DNA following the promoter is a gene and it contains the recipe for a protein. A mediator protein complex arrives carrying the enzyme RNA polymerase. It manoeuvres the RNA polymerase into place... inserting it with the help of other factors between the strands of the DNA double helix. The assembled collection of all these factors is referred to as the transcription initiation complex... and now it is ready to be activated. The initiation complex requires contact with activator proteins, which bind to specific sequences of DNA known as enhancer regions. These regions may be thousands of base pairs distant from the start of the gene. Contact between the activator proteins and the initiation-complex releases the copying mechanism. The RNA polymerase unzips a small portion of the DNA helix exposing the bases on each strand. Only one of the strands is copied. It acts as a template for the synthesis of an RNA molecule which is assembled one sub-unit at a time by matching the DNA letter code on the template strand. The sub-units can be seen here entering the enzyme through its intake hole and they are joined together to form the long messenger RNA chain snaking out of the top.