BOL: Related items

mutatrix: a population genome simulator which generates simulated genomes.

Jit — Tue, 28 Jan 2020 04:06:58 -0600

genome simulation across a population with zeta-distributed allele frequency, snps, insertions, deletions, and multi-nucleotide polymorphisms

More at https://github.com/ekg/mutatrix

./mutatrix -S sample -P test/ -p 2 -n 10 reference.fasta

Address of the bookmark: https://github.com/ekg/mutatrix

Internship Program for Bioinformatics / Biotechnology Professionals (No. Of Vacancy: 2)

Wed, 08 Oct 2014 01:10:08 -0500

ArrayGen is offering an Internship Program for Post graduate Bioinformatics / Biotechnology students and professionals. ArrayGen Technologies provide an excellent opportunity to gain research experience and explore if a scientific career is right for you. Currently we offer positions to outstanding students interested in Next Generation Sequencing (NGS) data analysis. Applications are accepted throughout the year. Accepted students will be listed on web with their schedules. Accepted students can attend our future workshops and trainings freely at the specified venue.

WEGO : simple but useful tool for visualizing, comparing and plotting GO (Gene Ontology) annotation results

BioStar — Sun, 12 Apr 2020 10:02:22 -0500

WEGO (Web Gene Ontology Annotation Plot) is a simple but useful tool for visualizing, comparing and plotting GO (Gene Ontology) annotation results. As the GO vocabulary became more and more popular, WEGO was widely adopted and used in many researches. Therefore we have updated WEGO 2.0 in 2018. Here are some changes we’ve made:
1. The limit of input file numbers was cancelled. Now the users could upload as many files as they want with one operation.
2. We have added the reference data of 9 species for users selection.
3. Besides the traditional WEGO histogram, WEGO 2.0 outputs an additional type of bar graph showing GO terms with significant gene number differences.

Address of the bookmark: http://wego.genomics.org.cn/

How far can bioinformatics go creating organisms used for testing?

Fri, 17 Oct 2014 02:08:16 -0500

"I think you can get very far on a technical level. The problem is that a human body is more complex than just one cell." ... "At some point we still need clinical tests on animals and humans before we use it for real treatment. But we will likely be able to remove 99 % of animal tests in the future." Erik Lindahl, Professor of Theoretical and Computational Biophysics at KTH Royal Institute of Technology is telling us about his work. From the episode "Science for life – mapping the building blocks of the human body". Watch the rest of the talk, and other talks at www.crosstalks.tv Crosstalks is an academic talkshow produced by KTH Royal Institute of Technology and Stockholm University.

dotPlotly: Generate an interactive dot plot from mummer or minimap alignments

Rahul Nayak — Thu, 21 Feb 2019 10:22:17 -0600

Create an interactive dot plot from mummer output OR PAF format

R script that makes a plotly interactive and/or static (png/pdf) dot plot.

Shiny app available for testing

Address of the bookmark: https://github.com/tpoorten/dotPlotly

Graduate research assistantships @ University of Nebraska-Lincoln (UNL)

Wed, 22 Oct 2014 10:05:31 -0500

Graduate research assistantships in quantitative genetics are available with Gota Morota in the Department of Animal Science at the University of Nebraska-Lincoln (UNL).

Current projects in the Morota lab include developing kernel-based whole-genome prediction and kernel-based genome-wide association models, polygenic modeling of binary traits, reexamining the results from quantitative genetics analysis in light of functional annotation, and extending kernel methods (such as GBLUP and RKHS) specifically tailored for diverse types of emerging omics data.

In addition, candidates will be expected to leverage opportunities to interact with faculty in animal genetics and biometrics at the UNL in the areas of bioinformatics, breeding, functional genomics, quantitative genetics, and molecular genetics.

Candidates should have a B.S. or M.S. degree in quantitative disciplines with strong background and interest in statistical computing.
The starting date is Fall 2015.
For more information about research in the Morota lab at the UNL, visit: http://www.morotalab.org

A letter of interest in the position, C.V., and contact information for
three references should be emailed to Gota Morota at .
Review of applications will begin immediately, and continue until the
positions are filled. Informal inquiries are also welcome.

Also, please see: http://animalscience.unl.edu/anscprospectivegraduatestudents

k-mers tutorial - classification and taxonomy

Neel — Thu, 26 Aug 2021 10:28:43 -0500

DNA k-mers underlie much of our assembly work, and we (along with many others!) have spent a lot of time thinking about how to store k-mer graphs efficiently, discard redundant data, and count them efficiently.

More recently, we've been enthused about using k-mer based similarity measures and computing and searching k-mer-based sketch search databases for all the things.

But I haven't spent too much talking about using k-mers for taxonomy, although that has become an ahem area of interest recently, if you read into our papers a bit.

In this blog post I'm going to fix this by doing a little bit of a literature review and waxing enthusiastic about other people's work. Then in a future blog post I'll talk about how we're building off of this work in fun! and interesting? ways!

Address of the bookmark: http://ivory.idyll.org/blog/2017-something-about-kmers.html

JRF/SRF at University of Calcutta

Fri, 31 Oct 2014 08:53:10 -0500

Applications are invited to appear at a walk-in-interview for one post of Junior Research Fellow in the DBT(DBT Twinning NER) sponsored project entitled “Protein folding kinetics is a selection force on shaping codon usage bias in the high expression genes” in the room of the HOD, Department of Biotechnology and the Coordinator, DR. B. C. Guha Centre for Genetic Engineering and Biotechnology, University College of Science, 35 Ballygunge Circular Road, Kolkata 700019 on the 12th November, 2014 at 3:00 p.m.

Essential qualifications: First class M. Sc. in any branch of life sciences and qualified CSIR-UGC NET/GATE Examination.

Desirable qualifications: Practical experience in biochemical and biophysical studies of proteins

Emoluments: as per DBT norms

The project is tenable for two years, initially for one year.

Age: Below 28 years (relaxable in the case of SC/ST/OBC/women candidates)

Candidates are requested to bring two sets of complete applications on plain paper furnishing bio-data and copies of attested certificates along with originals (for verification) on the date of interview.

No TA/DA is admissible for candidates appearing at the interview.

Dr. Rajat Banerjee
Assistant Professor
Department of Biotechnology and
Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology
University College of Science
35, Ballygunge Circular Road
Kolkata 700019

Advertisement: www.caluniv.ac.in/news/jrf_biotech_2.pdf

Biostats book !

Abhi — Mon, 14 Aug 2023 03:11:39 -0500

https://practical-stats-med-r.netlify.app/

Address of the bookmark: https://practical-stats-med-r.netlify.app/

JRF in Bioinformatics @ Pondicherry University

Sat, 08 Nov 2014 14:34:48 -0600

Eager to get JRF job in Puducherry? Pondicherry University, School of Life Sciences, Centre for Bioinformatics has issued notification to fill the vacancy of JRF for DST sponsored research project entitled "Design and discovery of aurora kinase inhibitors as anti cancer drugs; application of computer aided drug design". It is good chance to get job with Pondicherry University and secure your future. Learn eligibility criteria and apply on or before 21.11.2014.

Required Skills: no special skills required for this job post
Required Experience:
Experience in computer aided drug design and or biochemical testing of natural or synthetic compounds is desired
Required Education:
M.Sc. / M.Tech.

Required Job Profile:
Candidate must possess M.Sc. in bioinformatics or computational biology or biotechnology or any branch of life sciences or pharmacology or chemical sciences or M.Tech. in any branch of life sciences with at least fifty five percent marks with NET or GATE.

Desired Job Profile:
Candidate having experience in computer aided drug design and or biochemical testing of natural or synthetic compounds.

How to apply:
Eligible and interested candidates should need to appear for walk-in interview on 21.11.2014 at 1700 hrs at the above mentioned address.

Contact
Pondicherry University
Dr. S. Mohane Coumar, Assistant Professor & Project Investigator, Centre for Bioinformatics, Pondicherry University, Puducherry 605 014
Email:registrar@pondiuni.edu.in
Phone: 0413-2655175

More at http://www.pondiuni.edu.in/sites/default/files/JRF-bioinfor-041114.pdf