BOL: Related items

Minda: a tool for evaluating structural variant (SV) callers

LEGE — Sun, 31 Mar 2024 02:43:50 -0500

Minda is a tool for evaluating structural variant (SV) callers that

standardizes VCF records for compatibility with both germline and somatic SV callers,
benchmarks against a single VCF input file, or
benchmarks against an ensemble call set created from multiple VCF input files.

Address of the bookmark: https://github.com/KolmogorovLab/minda

LoVis4u: Locus Visualisation tool for comparative genomics

LEGE — Tue, 17 Sep 2024 02:30:57 -0500

Description

LoVis4u is a bioinformatics tool for Loci Visualisation.

LoVis4u, a command-line tool and Python API designed for highly customizable and fast visualisation of multiple genomic loci. LoVis4u generates vector images in PDF format based on annotation data from GenBank or GFF files. It is capable of visualising entire genomes of bacteriophages as well as plasmids and user-defined regions of longer prokaryotic genomes. Additionally, LoVis4u offers optional data processing steps to identify and highlight accessory and core genes in input sequences.

https://art-egorov.github.io/lovis4u/

Address of the bookmark: https://github.com/art-egorov/lovis4u

NanoSim: nanopore sequence read simulator based on statistical characterization.

Jit — Mon, 18 Dec 2017 04:16:31 -0600

NanoSim, a fast and scalable read simulator that captures the technology-specific features of ONT data and allows for adjustments upon improvement of nanopore sequencing technology. The first step of NanoSim is read characterization, which provides a comprehensive alignment-based analysis and generates a set of read profiles serving as the input to the next step, the simulation stage. The simulation stage uses the model built in the previous step to produce in silico reads for a given reference genome. NanoSim is written in Python and R. The source files and manual are available at the Genome Sciences Centre website: http://www.bcgsc.ca/platform/bioinfo/software/nanosim

https://github.com/bcgsc/NanoSim

Address of the bookmark: http://www.bcgsc.ca/platform/bioinfo/software/nanosim

Bioinformatics Scientist – ICMR Computational Genomics Centre

Sat, 26 Dec 2020 10:18:29 -0600

ICMR invites online applications, from Indian Citizens, up to 8th January 2020 till 5:30 PM to fill up the following post to be filled purely on a temporary basis under “ICMR Computational Genomics Centre” under Dr. Harpreet Singh, Head, Division of Biomedical Informatics (BMI), ICMR HQRS, New Delhi 110029.
The Terms & Conditions for the post are as follows:

a) Scientist-B – UR (2 posts-Bioinformatics) on consolidated salary of Rs.48,000/- pm + HRA

b) Scientist C – UR (1 post -Bioinformatics) on consolidated salary of Rs. 51,000 pm+ HRA

c) Scientist B- UR (2 post-Statistics) on a consolidated salary of Rs.48,000/- pm +HRA

d) Computer Programmer 1 post UR & 1 post SC on a consolidated salary of Rs. 32,500/- pm

e) Research Assistant -UR 1 post on a consolidated salary of Rs. 31,000/- pm

More at https://projectjobs.icmr.org.in/sccbioinformatics/uploads/recruitment/Adv_BMI_24122020.pdf

Computational Genomics: Applied Comparative Genomics

Jit — Wed, 29 Nov 2017 05:11:30 -0600

The primary goal of the course is for students to be grounded in theory and leave the course empowered to conduct independent genomic analyses. We will study the leading computational and quantitative approaches for comparing and analyzing genomes starting from raw sequencing data. The course will focus on human genomics and human medical applications, but the techniques will be broadly applicable across the tree of life. The topics will include genome assembly & comparative genomics, variant identification & analysis, gene expression & regulation, personal genome analysis, and cancer genomics. The grading will be based on assignments, a midterm exam, class presentations, and a significant class project. There are no formal course prerequisites, although the course will require familiarity with UNIX scripting and/or programming to complete the assignments and course project.

Address of the bookmark: https://github.com/schatzlab/appliedgenomics

3 PhD positions available in the area of Bioinformatics/Computational Biology at ulster.ac.uk

Thu, 02 Jan 2020 12:41:10 -0600

3 PhD positions available in the area of Bioinformatics/Computational Biology, Machine Learning (ML)/Artificial Intelligence (AI), Biomarker Discovery, Stratified/Personalized Medicine in Mental Health, Diabetes and Multimorbidity. Please see details (weblinks) below:

1. https://www.ulster.ac.uk/doctoralcollege/find-a-phd/510894
2. https://www.ulster.ac.uk/doctoralcollege/find-a-phd/511458
3. https://www.ulster.ac.uk/doctoralcollege/find-a-phd/512618

Looking for students with good computational/programming skills (preferable in Linux/Shell, Python and/or R) and knowledge in computational biology and statistics. However, students from more biology oriented background but strong interest to learn bioinformatics and programming are also encouraged to apply.

Informal inquiries are welcomed at: p.shukla@ulster.ac.uk

Dr Priyank Shukla PhD FHEA FCHERP
Lecturer (Asst Prof) in Stratified Medicine (Bioinformatics)

Northern Ireland Centre for Stratified Medicine
Biomedical Sciences Research Institute
University of Ulster (Magee Campus)
C-TRIC Building, Altnagelvin Area Hospital
Glenshane Road, Derry/Londonderry
BT47 6SB, Northern Ireland, United Kingdom

T: +44 28 7167 5690
E: p.shukla@ulster.ac.uk
W: https://www.ulster.ac.uk/staff/p-shukla

A computational postdoc position and a bioinformatician position

Thu, 18 Jan 2018 16:29:42 -0600

A computational postdoc position and a bioinformatician position are available in Alessandro Romanel's Lab recently established at the Centre for Integrative Biology (CIBIO) in Trento, Italy. The positions are in the context of an AIRC grant and are immediately available.

Successful candidates will be involved in the design and implementation of strategies to study the role of inherited polymorphisms in combination with timedependent variables and somatic events on cancer genesis, progression and resistance.
The ideal postdoc candidate will have a PhD in Computer Science, Bioinformatics, Computational Biology or equivalent, experience in the analysis of next generation sequencing and high-density array data from human cells, strong analytical and quantitative background and programming skills. Background in cancer genomics is recommended.
The ideal bioinformatician candidate will have a four or five years degree in Computer Science, Bioinformatics or equivalent, experience in the management of large datasets, implementation of processing pipelines and strong programming skills. Background in biology/genomics is a plus.
Highly motivated individuals are invited to send a detailed CV, a cover letter describing research interests and experience, and contact information for two references to Alessandro Romanel (alessandro.romanel@unitn.it).

RosettaAntibodyDesign (RAbD): A general framework for computational antibody design

BioStar — Sun, 20 Sep 2020 06:03:42 -0500

RosettaAntibodyDesign (RAbD) is a generalized framework for the design of antibodies, in which a user can easily tailor the run to their project needs. The algorithm is meant to sample the diverse sequence, structure, and binding space of an antibody-antigen complex. It can be used for a multitude of project types, from denovo design to redesigns that improve binding affinity, optimize stability, or manipulate function.

The framework is based on rigorous bioinformatic analysis and rooted very much on our recent clustering of antibody CDR regions. It uses the North/Dunbrack CDR definition as outlined in the North/Dunbrack clustering paper.

More at

https://www.rosettacommons.org/docs/latest/application_documentation/antibody/RosettaAntibodyDesign

https://bio-jade.readthedocs.io/en/latest/installation.html

Address of the bookmark: https://www.rosettacommons.org/docs/latest/application_documentation/antibody/RosettaAntibodyDesign

Want to Know which genome assembler rule the world ?

Rahul Agarwal — Sun, 11 Aug 2013 11:42:32 -0500

Assemblathon 2: evaluating de novo methods of genome assembly

http://www.gigasciencejournal.com/content/2/1/10/abstract

http://blogs.nature.com/news/2013/07/genome-assembly-contest-prompts-soul-searching.html

http://assemblathon.org/post/44431915644/feedback-and-analysis-of-the-assemblathon-2-p

The Story of You: ENCODE and the human genome

Sat, 24 Aug 2013 18:49:03 -0500

Ever since a monk called Mendel started breeding pea plants we've been learning about our genomes. In 1953, Watson, Crick and Franklin described the structure of the molecule that makes up our genomes: the DNA double helix. Then, in 2001, scientists wrote down the entire 3-billion letter code contained in the average human genome. Now they're trying to interpret that code; to work out how it's used to make different types of cells and different people. The ENCODE project, as it's called, is the latest chapter in the story of you. To read the ENCODE research papers and more, visit http://www.nature.com/ENCODE