BOL: Related items

AirLift, a methodology and tool for comprehensively moving mappings and annotations from one genome to another similar genome

Jit — Mon, 23 Dec 2019 10:20:13 -0600

We propose AirLift, a methodology and tool for comprehensively moving mappings and annotations from one genome to another similar genome while maintaining the accuracy of a full mapper.

Address of the bookmark: https://github.com/CMU-SAFARI/AirLift

Google Genomics

Reshma Khatun — Fri, 17 Oct 2014 02:14:14 -0500

Google Genomics provides an API to store, process, explore, and share DNA sequence reads, reference-based alignments, and variant calls, using Google's cloud infrastructure.

Store alignments and variant calls for one genome or a million.
Process genomic data in batch by running principal component analysis or Hardy-Weinberg equilibrium, in minutes or hours, by using parallel computing frameworks like MapReduce.
Explore data by slicing alignments and variants by genomic range across one or multiple samples -- for your own algorithms or for visualization; or interactively process entire cohorts to find transition/transversion ratios, allelic frequency, genome-wide association and more using BigQuery.
Share genomic data with your research group, collaborators, the broader community, or the public. You decide.

Google Genomics is implementing the API defined by the Global Alliance for Genomics and Health for visualization, analysis and more. Compliant software can access Google Genomics, local servers, or any other implementation.

Address of the bookmark: https://cloud.google.com/genomics/

Research Scientist – National Institute of Cholera and Enteric Diseases

Wed, 22 Oct 2014 10:26:46 -0500

The following post is to be filled up on purely temporary basis under the project entitled "Second phase of Task Force Biomedical Informatics Center of ICMR" under Dr. Santasabuj Das, Scientist 'D' of this Institute:-

01. Scientist II 01
Essential: Ph.D. degree in Life Sciences from a recognized university along with a minimum of 2 years of research experience in Bioinformatics as evidenced by publications in the peer reviewed journals.

OR
Ph.D. degree in Bioinformatics from a recognized university.

OR
M.Sc. in Bioinformatics from a recognized university along with a minimum of 3 years of research experience in Bioinformatics as evidenced by publications in the peer reviewed journals.

Desirable:
Thorough Knowledge about In silico genome analysis and comparative genomics.
Experience with in silico identification of novel virulence factors of pathogens, host-pathogen interactions and Systems Biology.
Additional Postdoctoral research experience in relevant subjects from a recognized institutions.

Rs. 44,000/- p.m. (consolidated) plus 30% HRA

Below 40 years

Applications along with Bio-Data containing detail work experience and full list of publications may be sent via email tosantasabujdas@yahoo.com latest by October 27, 2014.

Short-listed candidates will be called via email for an interview to be held at the institute in the second week of November, 2014.

Advertisement: www.niced.org.in/placements.htm

Postdoctoral fellowship in Bioinformatics

Sat, 08 Nov 2014 14:41:14 -0600

A two-year post-doctoral position is available in the Biocomputing group of the Sapienza University led by Anna Tramontano to work on either genomics research or structural bioinformatics, focusing on the study of relevant biomedical problems.
The ideal candidate should be motivated and talented, hold a PhD degree, have good programming skills, a grasp of statistical methods and an understanding of biology.
Experience in the development of computational biology methods would be an added value.

Good communication skills and fluency in spoken and written English are required.
Please apply sending a curriculum vitae, the names of at least two referees and a letter of motivation describing past experience and future goals to anna.tramontano@uniroma1.it with subject: “Application for post-doctoral position November 2014 YOUR LAST NAME”

Deadline: No later than November 28th, 2014.
Duration: 2 years

Salary on grant: Commeasured to the experience of the candidate
Contact Person (Referent): Anna Tramontano
Ref. E-Mail: anna.tramontano@uniroma1.it
Group Web Page: http:/www.biocomputing.it

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/

Bioinformatics JRF/RA/SRF position at Institute of Cytology and Preventive Oncology (ICPO)

Wed, 19 Nov 2014 20:16:32 -0600

Institute of Cytology and Preventive Oncology (ICPO) I-7, Sector-39, Noida-201301

Candidates having the below mentioned qualifications may appear for walk in interview at ICPO on 2nd December 2014 between 10.00 AM and 12:00 PM under the below time bound projects under Dr. Subhash M. Agarwal, Scientist C. The post is purely temporary and co-terminus with the project.

Research Assistant (One)
25650/- consolidated
Discovery of EGFR secondary mutant inhibitors using structure based screening approach (ICMR)
Duration: 7 months

Essential: M.Sc./ M.Tech in Bioinformatics or any other related subject with good academic record.

Desirable: Experience in scripting and molecular docking.

Below 30 years

Junior Research Fellow (One)

16,000 + 30% HRA = Rs. 20800/-

Identification of novel inhibitors targeting EGFR using an integrated ligand and structure based approach (DBT)

Duration: 9 months

Essential: M.Sc./ M.Tech in Bioinformatics or any other related subject with good academic record. Candidates with CSIR-UGC / ICMR, NET qualification will be preferred

Desirable: Experience in scripting, QSAR and molecular docking.

Below 28 years

Interested eligible candidates may send their applications with Bio-data by email at (smagarwal@gmail.com) or by post addressed to Dr. Subhash M Agarwal, Scientist C, Institute of Cytology and Preventive Oncology (ICPO) I-7, Sector-39, Noida-201301 so as to reach latest by 1st December, 2014. The candidates may appear for interview at ICPO along with 3 copies of CV, photo and relevant certificates of qualifications in original and reprints of publications at the time of interview. It should be noted that No TA/DA will be paid for the walk in Interview.

Advertisement: www.icpo.org.in/advt-walk-in-interview.docx

Genome Origami

Jitendra Narayan — Fri, 12 Dec 2014 22:48:17 -0600

There are several interesting factoid about our genomes, one of them is their folding. If we stretched out the DNA in a single cell, which is only a few millionths of an inch wide, it would span more than six feet. In other word, the size of six feet DNA fold themself to fit in a few millionths of an inch wide space. These DNA folding is a dynamic process that changes over time (!!). Researchers around the world have been trying to understand how DNA folds itself up so efficiently, and a recent post on the NIH Director’s Blog highlights new research illustrating how the human genome folds inside the cell’s nucleus, as well as how DNA folding affects gene regulation. The research team created this delightful video that demonstrates the principles involved using origami art.

http://bioinformaticsonline.com/videolist/watch/19555/a-3d-map-of-the-human-genome

Researchers have been working to determine how cells regulate gene expression for nearly as long as we’ve known about DNA. How, for example, do nerve cells know to turn off only nerve cell genes and turn off bone cell genes? DNA folding loops are part of the answer. This research team, which published their findings in a paper in Cell http://www.cell.com/cell/abstract/S0092-8674%2814%2901497-4 , found that the number of loops is much lower than expected. There are only 10,000 loops instead of the predicted millions, and they form on/off switches in DNA.

More at http://www.eurekalert.org/pub_releases/2014-12/ru-3mr121114.php

Reference http://www.cell.com/cell/abstract/S0092-8674%2814%2901497-4

odgi: optimized dynamic genome/graph implementation

Abhimanyu Singh — Tue, 01 Feb 2022 23:42:21 -0600

odgi provides an efficient and succinct dynamic DNA sequence graph model, as well as a host of algorithms that allow the use of such graphs in bioinformatic analyses.

Careful encoding of graph entities allows odgi to efficiently compute and transform pangenomes with minimal overheads. odgi implements a dynamic data structure that leveraged multi-core CPUs and can be updated on the fly.

The edges and path steps are recorded as deltas between the current node id and the target node id, where the node id corresponds to the rank in the global array of nodes. Graphs built from biological data sets tend to have local partial order and, when sorted, the deltas be small. This allows them to be compressed with a variable length integer representation, resulting in a small in-memory footprint at the cost of packing and unpacking.

The RAM and computational savings are substantial. In partially ordered regions of the graph, most deltas will require only a single byte.

Address of the bookmark: https://github.com/pangenome/odgi

WALK – IN – INTERVIEW @ Agricultural Knowledge Management Unit Indian Agricultural Research Institute, New Delhi-110012

Fri, 12 Dec 2014 21:33:02 -0600

Walk-in-interview for the following temporary positions will be conducted on 20th December 2014 (between 10:00 AM to 01:00 PM) at Agricultural Knowledge Management Unit, A0 block (Ground Floor), LBS Building, Indian Agricultural Research Institute, New Delhi-110012:

1 Dr. A.K.Mishra Coordinator & PI (BTISnet)

Traineeship (two) for one year

Rs. 5000/- (consolidated)

M.Sc. (Bioinformatics) with 60 % marks from a recognized University

20-12-2014 (10:00 AM -11:00 AM)

Studentship (four) for one year

Rs. 2500/- (consolidated)

Final year M.Sc./ M.Tech (Bioinformatics) Students from a recognized University

20-12-2014 (11:00 AM- 1:00 PM)

The positions are purely temporary and co-terminus with the DBT Programme. Eligible candidates are requested to submit the application form in the prescribed format along with original certificates/ documents (Degree, Marks sheets, Work experience, if any) at the time of interview. No TA/DA will be paid. Maximum age limit is 28 years for all positions. Age relaxation of 5 yrs for SC/ST and woman candidates and 3 years for OBC candidates will be given. Canvassing in any form invites disqualification.

Advertisement: http://www.iari.res.in/files/BIC-08122014-20141208-172344.pdf

Genomicus: genome browser that enables users to navigate in genomes in several dimensions

Jit — Mon, 28 Feb 2022 23:27:37 -0600

Genomicus is a genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.

Once a query gene has been entered, it is displayed in its genomic context in parallel to the genomic context of all its orthologous and paralogous copies in all the other sequenced metazoan genomes. Moreover, Genomicus stores and displays the predicted ancestral genome structure in all the ancestral species within the phylogenetic range of interest.

All the data on extant species displayed in this browser are from Ensembl.

Summary statistics of Genomicus version 105.01: (view species tree in pdf or newick)


Number of extant species	200
Number of extant genes	4303993
Number of ancestral species	196
Number of ancestral genes	4624213
Number of ancestral synteny blocks	83342

Address of the bookmark: https://www.genomicus.bio.ens.psl.eu/genomicus-105.01/cgi-bin/search.pl