BOL: Related items

Pimp your brain: Bioinformatics

Wed, 20 Aug 2014 22:09:21 -0500

Jan Lisec from the Max Planck Institute of Molecular Plant Physiology explains, in this "pimp your brain" episode, what bioinformatics is and why bioinformatics is so important and indispensable for biological research. In the video serial "Pimp your brain" scientists from the Max Planck Institute of Molecular Plant Physiology describe their research. More videos from the 'Pimp your brain' serial are available on www.youtube.com/playlist?list=PL-l9VItC9Gn2Ur2Xj6PTOAkjLUlVPbIOO More videos are available on www.mpimp-golm.mpg.de

pWhatsHap: a parallel, high-performance version of WhatsHap

Jit — Wed, 14 Nov 2018 08:20:27 -0600

Given the potential relevance of efficient haplotyping in several analysis pipelines, we have designed and engineered pWhatsHap, a parallel, high-performance version of WhatsHap. pWhatsHap is embedded in a toolkit developed in Python and supports genomics datasets in standard file formats. Building on WhatsHap, pWhatsHap exhibits the same complexity exploring a number of possible solutions which is exponential in the coverage of the dataset. The parallel implementation on multi-core architectures allows for a relevant reduction of the execution time for haplotyping, while the provided results enjoy the same high accuracy as that provided by WhatsHap, which increases with coverage.

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1170-y

Address of the bookmark: https://bitbucket.org/whatshap/whatshap

Center for Molecular Dynamics Nepal (CMDN), Nepal

Wed, 23 Jul 2014 13:54:51 -0500

Center for Molecular Dynamics Nepal (CMDN), established 2007 prides itself as a research driven nongovernmental organization. Unlike other civil society organizations, CMDN is dedicated entirely to promoting research in the country. With its team of energetic and highly motivated experts, CMDN is now recognized as the leading public health and wildlife research organization of the country.

More at http://www.cmdn.org.np/main/index.php

Genome Annotation using MAKER tutorial !

Shruti Paniwala — Thu, 20 Dec 2018 17:39:23 -0600

MAKER is a great tool for annotating a reference genome using empirical and ab initiogene predictions. GMOD, the umbrella organization that includes MAKER, has some nice tutorials online for running MAKER. However, these were quite simplified examples and it took a bit of effort to wrap my head completely around everything. Here I will describe a de novo genome annotation for Boa constrictor in detail, so that there is a record and that it is easy to use this as a guide to annotate any genome.

Address of the bookmark: https://www.biostars.org/p/261203/

Senior Research Fellow at NIT, Rourkela

Wed, 30 Jul 2014 00:53:13 -0500

NATIONAL INSTITUTE OF TECHNOLOGY, ROURKELA – 769 008(ORISSA)
SPONSORED RESEARCH, INDUSTRIAL CONSULTANCY & CONTINUING EDUCATION

ADVERTISEMENT NO: NITR/SR/CH-BIF/2014/30

Applications are invited on prescribed format for the following assignment in a purely time bound research project undertaken in the Department of Biotechnology & Medical Engineering of the Institute.

1. Name of the Temporary Post : Senior Research Fellow-01
2. Name of the Research Project: “ Bioinformatics Infrastructure Facility (BIF)”
3. Name of the Sponsoring Agency: DBT, Government of India, 4 Tenure of the Project : 12th Five year Plan
5 Tenure of the Assignment : 01 year [Likely to be extended for 04 more years]
6 Job Description : BIF Maintenance and Active Research in Bioinformatics
7. Consolidated monthly compensation / Fellowship: Rs.18,000/- P.M.

8. Essential Qualifications and experience: B.Tech with valid GATE Score or M.Tech degree in Biotechnology/Bioinformatics/Computer Science/Computational Biology
9. Desirable Qualifications/ Experiences: Experience of Programming in PERL,R, Python, Unix and Visual Studio + Knowledge in NGS data analysis work flows ,WGS and statistical packages such as CRAN-R,MATLAB etc.

10. Accommodation : Bachelor accommodation in the Institute may be provided subject to availability.
11. For technical information on the project, the candidate may contact the Principal Investigator at the following address:

Name : Prof. Mukesh K Gupta
Address : Dept. of Biotechnology & Medical Engineering,
N.I.T.Rourkela-769 008
Telephone No : 0661-2462294
E-mail : guptam@nitrkl.ac.in

Eligible persons may apply in the prescribed format (available in the Institute Website)affixed with coloured photographs to be submitted in duplicate along with photo copies of relevant certificates, grade/ mark sheets, publications etc., to Asst. Registrar, SRICCE,
National Institute of Technology, Rourkela–769 008 before 22.08.2014. The cover should be super- scribed clearly the post applied for & Name of the Project.

Mere possession of minimum qualification does not guarantee invitation to the interview.
Candidates will be short listed based on merit and need of the project.

http://www.nitrkl.ac.in/IntraWeb/Jobs_Tenders/Jobs/ProjectFellowship/2014/141707192838_1.pdf

Genome assembly forensics: finding the elusive mis-assembly

Jit — Sat, 26 Jan 2019 18:02:01 -0600

We present the first collection of tools aimed at automated genome assembly validation. This work formalizes several mechanisms for detecting mis-assemblies, and describes their implementation in our automated validation pipeline, called amosvalidate. We demonstrate the application of our pipeline in both bacterial and eukaryotic genome assemblies, and highlight several assembly errors in both draft and finished genomes. The software described is compatible with common assembly formats and is released, open-source, at http://amos.sourceforge.net.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2397507/

http://amos.sourceforge.net/wiki/index.php/AMOS

Address of the bookmark: http://amos.sourceforge.net/wiki/index.php/AMOS

MEGADOCK 4.0

Suleman Khan — Thu, 07 Aug 2014 18:08:54 -0500

An ultra–high-performance protein–protein docking software for heterogeneous supercomputers

Summary: The application of protein–protein docking in large-scale interactome analysis is a major challenge in structural bioinformatics and requires huge computing resources. In this work, we present MEGADOCK 4.0, an FFT-based docking software that makes extensive use of recent heterogeneous supercomputers and shows powerful, scalable performance of over 97% strong scaling.

Availability and Implementation: MEGADOCK 4.0 is written in C++ with OpenMPI and NVIDIA CUDA 5.0 (or later) and is freely available to all academic and non-profit users at: http://www.bi.cs.titech.ac.jp/megadock.

Contact: akiyama@cs.titech.ac.jp

Address of the bookmark: http://bioinformatics.oxfordjournals.org/content/early/2014/08/06/bioinformatics.btu532.short

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/

GrapheR !!!

John Parker — Thu, 14 Aug 2014 14:02:17 -0500

What a wonderful gem GrapheR is.... Oh yes it is. GrapheR is a GUI for base graphics in R by http://www.maximeherve.com/. The package provides a graphical user interface for creating base charts in R. It is ideal for beginners in R, as the user interface is very clear and the code is written along side into a text file, allowing users to recreate the charts directly in the console.

Adding and changing legends? Messing around with the plotting window settings? It is much easier/quicker with this GUI than reading the help file and trying to understand the various parameters.
Here is a little example using the iris data set.

library(GrapheR)
data(iris)
run.GrapheR()

This will bring up a window that helps me to create the chart and tweak the various parameters.

Finally, I find the underlying R code in a file created by GrapheR. For more details read also the package vignette, which is available in English, French and German!

Genome Informatics Section Lab !

Sat, 25 Jan 2020 06:38:23 -0600

Our section develops and applies computational methods for the analysis of massive genomics datasets, focusing on the challenges of genome sequencing and comparative genomics. We aim to improve such foundational processes and translate emerging genomic technologies into practice.

The Genome Informatics Section is hiring! Come join our outstanding team at the NIH’s National Human Genome Research Institute and contribute to the development of new reference genomes and computational methods for DNA sequencing and analysis. Both postdoc and PhD students positions are available. More information and application instructions follow below.

More at https://genomeinformatics.github.io/