BOL: Related items

snakepipes: A toolkit based on snakemake and python for analysis of NGS data

Jit — Thu, 30 May 2019 04:06:13 -0500

snakePipes are flexible and powerful workflows built using snakemake that simplify the analysis of NGS data.

DNA-mapping*
ChIP-seq*
RNA-seq*
ATAC-seq*
scRNA-seq
Hi-C
Whole Genome Bisulfite Seq/WGBS

(*Also available in "allele-specific" mode)

snakePipes can be installed via conda :

'conda install -c mpi-ie -c bioconda -c conda-forge snakePipes'.

Source code (https://github.com/maxplanck-ie/snakepipes) and documentation (https://snakepipes.readthedocs.io/en/latest/) are available online.

Address of the bookmark: https://github.com/maxplanck-ie/snakepipes

Sr. Scientist Bioinformatics Vacancies at Indian Institute of Toxicology Research, India

Tue, 01 Sep 2020 07:21:04 -0500

Start date of online Registration: Wednesday August 19, 2020 11:00 Hrs IST
Last date for Registration: Monday September 21, 2020 17:30 Hrs IST
Last date for submission of online application: Monday September 21, 2020 17:30 Hrs IST
Last date of Receipt of physical copy of application at CSIR-IITR: Tuesday October 05, 2020 17:30 Hrs IST

Pay Matrix Level-12
No. of Post-01
(UR)
Post – Sr. Scientist
Area Bioinformatics
Age limit : 37 years
PhD in Computational Biology/Bioinformatics with 2 years experience in desired area
Or
ME/M.Tech in Bioinformatics or Genome Informatics or Genetic Engineering with 3 years experience in desired area
Experience of understanding fundamental science behind Artificial Intelligence, machine learning, novel Artificial Intelligence algorithms and architectures, software engineering principles for Artificial Intelligence, natural language processing with proficiency in programming as evident by publications in SCI journals with high impact factor. To be part a group of scientists working in the area of genomics, running the central
bioinformatics facility, developing independent projects and providing bioinformatics support to the user scientists of the Institute.

More at

http://14.139.62.50/CSIR-IITR%20Scientist%20Recruitment%20Adv%202020.pdf

Bioinformatics jobs at Acrannolife

Sun, 25 Oct 2020 22:51:35 -0500

Acrannolife are looking for skilled Bioinformatics Scientists with a minimum of 2yrs Experience in NGS data analysis including Nanopore Sequencing.

This is an opportunity to work on projects that would fundamentally alter the way certain chronic conditions are treated and monitored.

About acrannolife:

We are a team of Post Docs, PhDs, Engineers, Clinicians, and MBAs working towards a future where biology intersects with software(Computational Biology).

We are incubated in Atal Incubation Centre - CCMB and have been backed by some of the leading thought leaders ranging from business to clinical practices.

Interested candidates can fill this form. https://lnkd.in/gtq47hy

and send their CV to hr@acrannolife.com

Dahak: benchmarking and containerization of tools for analysis of complex non-clinical metagenomes.

BioStar — Thu, 09 Apr 2020 04:56:09 -0500

Dahak is a software suite that integrates state-of-the-art open source tools for metagenomic analyses. Tools in the dahak software suite will perform various steps in metagenomic analysis workflows including data pre-processing, metagenome assembly, taxonomic and functional classification, genome binning, and gene assignment. We aim to deliver the analytical framework as a robust and reliable containerized workflow system, which will be free from dependency, installation, and execution problems typically associated with other open-source bioinformatics solutions. This will maximize the transparency, data provenance (i.e., the process of tracing the origins of data and its movement through the workflow), and reproducibility.

More at https://dahak-metagenomics.github.io/dahak/

Address of the bookmark: https://github.com/dahak-metagenomics/dahak

Postdoc in comparative genomics

Tue, 08 Dec 2020 09:26:40 -0600

We are looking for a highly motivated researcher for an 18 month postdoctoral position collaborating in an exciting project on comparative genomics of marine fish and shellfish species. In the project, we use genome resequencing data from a range of species to reconstruct the demographic history and characterize genomic signals associated with population divergence and local adaptation in high gene flow scenarios. The work will improve our understanding of interacting evolutionary processes and provide valuable data for securing sustainable management and conservation of exploited resources. Applicants are encouraged to develop their own research ideas within this framework.

The fellowship is part of a larger Nordic collaborative project, MarGen_II, financed by the EU Interreg Öresund-Kattegat-Skagerrak Programme, the Danish Rod and Net License Funds and the National Institute of Aquatic Resources (DTU Aqua). The project will primarily be carried out in the population genetics group, Section for Marine Living Resources, situated in Silkeborg, Denmark. DTU Aqua is an institute at the Technical University of Denmark. In addition, the position offers many opportunities for collaborating with Nordic and other European colleagues in the field.

Application:
Apply online at
https://www.dtu.dk/english/About/JOB-and-CAREER/vacant-positions/job?id=d198fd80-4856-4a56-943d-485106026504.
The deadline is 4 January 2021. For further information, please contact
Senior Researcher Jakob Hemmer-Hansen, jhh@aqua.dtu.dk.

You can read more about DTU Aqua at www.aqua.dtu.dk
and the population genetics group at
https://www.aqua.dtu.dk/english/research/population_genetics.

All interested candidates irrespective of age, gender, race, disability,
religion or ethnic background are encouraged to apply.

Jakob Hemmer Hansen

DnaSP: DNA Sequence Polymorphism, is a software package for the analysis of DNA polymorphisms

Neel — Wed, 25 Nov 2020 19:51:38 -0600

DnaSP, DNA Sequence Polymorphism, is a software package for the analysis of DNA polymorphisms using data from a single locus (a multiple sequence aligned -MSA data), or from several loci (a Multiple-MSA data, such as formats generated by some assembler RAD-seq software). DnaSP can estimate several measures of DNA sequence variation within and between populations in noncoding, synonymous or nonsynonymous sites, or in various sorts of codon positions), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters.

Address of the bookmark: http://www.ub.edu/dnasp/

ICGEB Bioinformatics Job

Sat, 23 Jan 2021 21:01:55 -0600

The following vacancies are available in the various ongoing bioinformatics projects at.
Translational Bioinformatics Group (https://www.icgeb.org/dinesh-gupta/), ICGEB, New Delhi, India. Shortlisted candidates will be welcomed for an on-line interview at ICGEB. Only the chosen applicants will be informed individually. Preference will be given to the applicants with experience related to Bioinformatics as well as Computational area.

Interested applicants must submit their complete, updated Curriculum Vitae, mentioning details of two references as well as various other details at – http://14.139.62.220/survey/index.php/2021/01/21/icgeb-dbt-project-vacancy/

The last date of submission of applications is January 31st, 2021.

Research Associate : PhD. Degree in Computational Biology/Bioinformatics.

Consolidated Salary: 58280/- pm (including HRA).

More at https://www.icgeb.org/project-positions-translational-bioinformatics-group/ and https://www.icgeb.org/category/vacancies/

GenomeTools: The versatile open source genome analysis software

Neel — Wed, 02 Feb 2022 04:00:21 -0600

The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named “libgenometools” which consists of several modules.

If you are interested in gene prediction, have a look at GenomeThreader.

http://genometools.org/pub/

Address of the bookmark: http://genometools.org/

Bioinformatics in Africa: Part3 - Mali

BioStar — Sat, 06 Feb 2021 13:28:44 -0600

International Center for Excellence in Research (ICER):

The ICER is a research center composed of the following three programs: 1. The Malaria Research and Training Center Parasitology Group, 2. The Malaria Research and Training Center Entomology Group 3. The SEREFO Group.

The first two programs develop biomedical researches in malaria, Filariasis and Leishmaniasis. The third program develops biomedical researches in tuberculosis and HIV.

Bioinformatics was introduced recently to the ICER and is constantly growing. The ICER has one team, headed by Sidy SOUMARE, which supports the three programmes in all their needs in informatics and bioinformatics. This team can beneficiate from some computational facilities (4 blast servers, 15 other servers and around 200 terminals), but the ICER staff needs some training in order to be able to administrate these facilities.

Research Interest and Activities: The following are the present areas of research interest: 1. Functional genomics 2. Analysis of microarray data 3. Interaction between the vector and the parasite.

Calculate the significance of the difference between two trends

BioStar — Tue, 14 Mar 2023 05:41:53 -0500

To calculate the significance of the difference between two trends, you can use a statistical test such as a t-test or ANOVA (analysis of variance). Here are the general steps to follow:

Define your null hypothesis (H0) and alternative hypothesis (H1). For example, H0 might be that there is no significant difference between the two trends, while H1 might be that there is a significant difference.
Collect data on the two trends. Make sure that the data is independent, normally distributed, and has equal variances.
Calculate the means and standard deviations of each trend.
Calculate the test statistic using a t-test or ANOVA. The test statistic will depend on the specific test you choose, but it will generally compare the difference in means between the two trends to the variability within each trend.
Determine the p-value associated with the test statistic. The p-value represents the probability of obtaining a test statistic as extreme as the one you calculated, assuming that the null hypothesis is true.
Compare the p-value to your chosen significance level (usually 0.05 or 0.01). If the p-value is less than or equal to the significance level, reject the null hypothesis and conclude that there is a significant difference between the two trends. If the p-value is greater than the significance level, fail to reject the null hypothesis and conclude that there is not enough evidence to support a significant difference.

It's important to note that the specific details of each step will depend on the type of test you choose and the software you use to perform the analysis.

The most common methods for comparing means include:

Methods	R function	Description
T-test	t.test()	Compare two groups (parametric)
Wilcoxon test	wilcox.test()	Compare two groups (non-parametric)
ANOVA	aov() or anova()	Compare multiple groups (parametric)
Kruskal-Wallis	kruskal.test()	Compare multiple groups (non-parametric)