BOL: Related items

China’s BGI says it can sequence a genome for just $100

Neel — Sat, 29 Feb 2020 04:49:43 -0600

Using technology originally acquired in the US, the Chinese gene giant BGI Group says it will make genome sequencing cheaper than ever, breaking the $100 barrier for the first time.

The Shenzhen company says the low cost will be possible with an “extreme” DNA sequencing system it plans to offer that is capable of decoding the genomes of 100,000 people a year.

Ref: https://www.technologyreview.com/s/615289/china-bgi-100-dollar-genome/

Edwards Lab

Sun, 10 Nov 2013 15:07:08 -0600

We study the evolutionary biology of birds and relatives, combining field, museum and genomics approaches to understand the basis of avian diversity, evolution and behavior. Our guiding approaches include population genetics, which provides a quantitative framework for studying speciation, geographic variation and genome evolution; systematics, which acknowledges that the focal species of any study has relatives that are behaviorally and ecologically no less interesting; and natural history, which gives meaning to the genes and genomic patterns we study.

Lab page: http://www.oeb.harvard.edu/faculty/edwards/index.html

Svardal lab

Sat, 20 Feb 2021 10:01:19 -0600

In the Svardal lab they are interested how the astonishing natural diversity we see on earth came into being, by which forces it formed and how it is changing today. Hence, they are trying to understand the process of evolution, with mathematical models and through the analysis of genome sequencing data.

Genomes, and in particular differences between them, are a crucial source of information to understand evolution and biology in general. They provide a record of the evolutionary past of populations, their relatedness patterns, their demography, and their adaptations.

More at https://www.uantwerpen.be/en/staff/hannes-svardal/svardal-lab/

Ai-CADD Project @ Kerela University

Tue, 19 Nov 2013 17:48:15 -0600

Applications are invited for the following Positions in the AiCADD project funded by MHRD Govt of India

Last Date for Submitting Application: 25th November 2013

1. Senior Scientist: (01 position)
Pay Scale: Rs.40, 000/-
Qualifications: PhD/ Post Doctoral with Experience in CADD

2. Junior Scientist (10 positions)
Pay Scale: Rs. 22,000/-
Qualifications: MPhil / Masters Degree in Bioinformatics / Computational Biology / CADD / Ayurveda

3. Technical Assistant (01+01 positions)
Pay Scale: Rs.12,000/-
Qualifications: 1. BSc Computer Science/ MCA
Qualifications: 2. MSc Biotechnology / MSc Microbiology

4. Programmer (01 position)
Pay Scale: Rs.20,000/-
Qualifications: MSc Computer Science/ MCA / B Tech (Experience in MATLAB, C, C++) Industrial experience is desirable

5. Teaching Assistant (03 positions)
Pay Scale: Rs.10,000/-
Qualifications: MSc in Bioinformatics

6. Administration Assistant (02 positions)
Pay Scale: Rs.8,000/-
Qualifications: Degree + PGDCA

The Selection process comprises of written test and interview. Positions are purely temporary (initially for the period of one year) and co-terminus with the project. For more details mail to: cbi.uok [at] gmail.com

More detail @ https://sites.google.com/site/centreforbioinformatics/announcements/applicationsinvitedforapplicationforai-caddproject

Calling variants in non-diploid systems

Neel — Sat, 26 Jun 2021 15:37:49 -0500

The main challenge associated with non-diploid variant calling is the difficulty in distinguishing between the sequencing noise (abundant in all NGS platforms) and true low frequency variants. Some of the early attempts to do this well have been accomplished on human mitochondrial DNA although the same approaches will work equally good on viral and bacterial genomes (Rebolledo-Jaramillo et al. 2014, Li et al. 2015).

Address of the bookmark: https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/non-dip/tutorial.html

Scientist-B @ VECTOR CONTROL RESEARCH CENTRE

Tue, 19 Nov 2013 21:19:15 -0600

VECTOR CONTROL RESEARCH CENTRE
(Indian Council of Medical Research)
Indira Nagar Medical Complex
Puducherry-605006

WALK-IN-INTERVIEW

The following vacancies shall be filled purely on adhoc basis under Non-Institutional adhoc project “Bioinformatics in ICMR Institutes” funded by Indian Council of Medical Research at Vector Control Research Centre, Puducherry, to be renewed annually and filled through Walk-in-Interview as indicated below. Candidates who wish to appear for the Walk-in-Interview can download the application format given in the website of Vector Control Research Centre (www.vcrc.res.in). Duly filled in application along with attested copies of certificate should be submitted at time of interview.

Date & Time : 05.12.2013 at 9.00 AM – Scientist-C (Non-Medical)

05.12.2013 at 1.30 PM – Scientist-B (Non-Medical)
06.12.2013 at 9.00 AM – Technical Assistant (Research Assistant)
06.12.2013 at 1.30 PM – Multi Tasking Staff (General)

Place : Vector Control Research Centre, Puducherry

Project entitled : Biomedical Informatics Centres of ICMR

1. Scientist - C (Non-Medical) Number of post – ONE

Essential qualification

B.E./ B. Tech. Degree in Bioinformatics/ Computational Biology from a recognized University with 6 years experience in the relevant field OR

First class Master’s Degree and Ph.D. Degree in Bioinformatics/ Computational Biology from a recognized University OR

First class Master’s Degree in Bioinformatics/ Computational Biology from a recognized University with 4 years R & D experience in the related subjects as mentioned above OR

Second class Master’s Degree + Ph.D. in Bioinformatics/ Computational Biology from a recognized University with 4 years research experience in bio-medical subjects

Age: Not exceeding 40 years Consolidated Salary – Rs.39,960/- p.m. + HRA as
admissible

Desirable qualification (i) Post-doctorate in Bioinformatics/ Computational Biology or M.E. / M. Tech. Degree in Bioinformatics/ Computational Biology from a recognized University for candidates with First Class relevant degree.

(ii) Additional post-doctoral research / teaching experience in Bioinformatics/Computational Biology in recognized Institute(s).

(iii) Knowledge of computer applications or data management

Job requirements i) To apply Bioinformatics / Computational Biology tools in understanding interactions between vectors and parasites/ pathogens and target based development of drug / insecticides.

ii) To assist the investigators to carry out genomic studies on parasites/pathogens/vectors of vector borne diseases

Advertisement: http://vcrc.res.in/Adv_Bio13.pdf

ncbi-datasets-cli -- Quickstart: command line tools !

Jit — Tue, 07 Dec 2021 02:51:26 -0600

Install and use the NCBI Datasets command line tools

The NCBI Datasets datasets command line tools are datasets and dataformat .

Use datasets to download biological sequence data across all domains of life from NCBI.

Use dataformat to convert metadata from JSON Lines format to other formats.

Conda download:

https://anaconda.org/conda-forge/ncbi-datasets-cli

Buld Download

https://www.ncbi.nlm.nih.gov/datasets/builder/?tax_id=29979

Address of the bookmark: https://www.ncbi.nlm.nih.gov/datasets/docs/v1/quickstarts/command-line-tools/

Roslin Bioinformatics Group

Mon, 25 Nov 2013 23:55:25 -0600

Roslin Bioinformatics Group

The Law group provides internal Institute-specific development, training and support roles for data manipulation, sequence analysis and any other aspect of the analysis of biological data using computer systems. Additionally we provide databases and applications supporting the international animal science community, particularly tools and resources for genome mapping.

Head: Andy Law. Members: John Bowman (animal facility database applications), Zen Lu (bioinformatics support), Trevor Paterson (software development)

More @ http://www.bioinformatics.ed.ac.uk/groups/roslin-bioinformatics-group

PhD at University of Calgary

Fri, 27 Dec 2013 20:24:39 -0600

Institution/Company:
University of Calgary
Location:
Calgary, AB
Job Description:

Novel diagnostic platform for detection of Osteoarthritis

I invite applications from highly motivated individuals to join my laboratory as a PhD student in Systems Biology at the University of Calgary McCaig Institute for Bone and Joint Health. This project is aimed at characterizing the networks of physical (protein-protein) interactions underlying inflammatory processes in patients with Osteoarthritis and how this differs from patients with Rheumatoid Arthritis and normal individuals. This work will eventually lead to the development of a novel diagnostic platform for the non-invasive and accurate detection of early Osteoarthritis. The selected candidate will use state-of-the-art computational methodologies to systematically analyze proteomic data, and develop /implement new algorithms to identify protein and functional interaction networks from high throughput experimental data. The individual will also benefit by working closely with experts at the UofC and UofA through an AIHS Alberta Osteoarthritis Team Grant which includes experts from all pillars of health research. The candidate will also be supported to attend bioinformatics workshops and conferences to advance and disseminate their research.
Qualifications: The ideal candidate will have a Master’s degree in Computational Biology, Bioinformatics, or equivalent with strong background knowledge of the Biological Sciences, Biochemistry, and Microbiology. The individual should additionally have experience in handling high-throughput data sets as well as programming skills. The candidate will be registered as a PhD student in Dr. Krawetz’s laboratory, located in the new state-of-the-art Health Research Innovation Centre at the UofC. The individual will have strong verbal and written skills and the ability to work efficiently in a team environment.

In addition to the outstanding research opportunities available in this setting, students also enjoy the many cultural and sporting amenities provided in the city of Calgary, and can take advantage of the unparalleled skiing and hiking in the Rocky Mountains that are less than an hour away.

Candidates must be academically competitive and will be expected to apply for external funding. The stipend is $25,000/yr. For outstanding PhD students, internal top-up award opportunities are available on a competitive basis. If interested in joining the lab, please contact Dr. Krawetz directly at rkrawetz@ucalgary.ca and provide the following information:

- Short cover letter explaining your interest in the lab
- Resume
- Scanned copy of transcript or listing of course grades
- Names and contact information for two individuals who will be willing to provide letters of reference

Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data

Neel — Fri, 25 Feb 2022 04:42:09 -0600

This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc.

Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example:

Address of the bookmark: https://github.com/KamilSJaron/smudgeplot