BOL: Related items

Five key traits to seek out in potential bioinformatics candidates !!!

Jit — Mon, 10 Aug 2015 12:53:50 -0500

Genomics and proteomics data are being collected in bulk, but mostly, traditional biologist don’t know what to do with it. Perhaps this is the reason why (not only this!!! ) computational biologist/bioinformatics scientists are hot commodities in the research world.

In fact, there are huge demands for expert biological data analyst. It’s a fairly new (not exactly) hot area, these bioinformatician are invaluable because they know and understand the significance of biological data for your research and how you can use it for better understanding of biological problems.

The bioinformatics can discover biological patterns and stories in genomic and proteomics data. They can develop the pipeline needed to properly collect, store and analyse it.

Once your research group is ready to make a larger investment and hire a bioinformatician to gain a competitive edge, there are several key traits to seek out in potential candidates. The best bioinformatician are:

1. Highly Skilled - programming skills, experience with the biological software and tools.

The biological data won’t illuminate much if the scientist analysing it doesn’t possess practical programming skills, experience with the biological software and tools and a thorough understanding of basic biological stuff. A solid background in mathematics and statistics is also an indispensable trait.

2. Insight - Real vision, robust understanding and deep insight.

In order to hire the best bioinformatics and computational biologist scientist for your needs, it is always recommended and mostly practiced by the recruiters, to ask each contender to write and develop a sample script/presentation based on a specific set of data you provide. Then, explore the approaches used to deal with data provided and pick up those candidates who convey real vision, robust understanding and deep insight.

3. Energetic – Curiosity to explore

Mostly natural curiosity and enthusiasm for solving big biological problems coupled with an ability to transform data into a scientific stories may place one candidate above the rest. In addition to achieve that, the bioinformatician should be agile enough to quickly modify their methods to suit changes within a particular research.

4. Researcher – Publications

Look for someone who has a keen sense and understanding of concern biological problems. You can judge it by looking at previously published papers and data. It is always recommended to have a look at GitHub and other repository for codes written by her/him.

5. Impressive communicator - Insight that can’t be expressed is worthless.

Good bioinformatics scientists are able to uncover biological patterns and are willing to explain those patterns in clear and helpful ways through thoughtful and open communication. In other words, they should must have good scientific writing skills. A computational biologis/bioinformatician should know how to present the data and tell a scientific story through numbers/images.

Scientist-B (Bioinformatics) at AIIMS, Delhi

Sun, 20 Dec 2020 04:34:55 -0600

Name of the Project: “Artificial intelligence in Oncology, Harnessing big data and advanced computing to provide personalized diagnosis and treatment for Cancer patients”

Age Limit: 35

How to Apply for the AIIMS Life Science Job:

Interested applicants are asked to send out a detailed CV to Dr Ashok Sharma (aioncoaiims@gmail.com). Laboratory of Chromatin and also Cancer Epigenetics, Department of Biochemistry with the subject line “Application for Scientist-B position for MeitY project” latest by January 01st, 2021.
Complete Information of the year of passing, experience, marks, etc. ought to be mentioned in the CV Incomplete. applications will certainly be rejected Just shortlisted applicants will be called for interview. Chosen candidates will certainly be intimated by email/phone.
No TA/DA will certainly be paid for appearing in the interview.
Note, The institute reserved the right to fill up or not to fill up the post advertised.

Emoluments: Rs. 56,000/- plus 24 percent HRA

Eligibility:
2nd class Master’s Degree with a PhD in a pertinent subject (Bioinformatics) from.a recognized University
1st class Master’s degree in Life Sciences (Bioinformatics) from a recognized university OR.
Bachelor’s Degree in Engineering or-Technology with minimal 60% marks from a recognized University or equivalent.

Desirable Qualifications:
Experience in Bioinformatics/NGS data. Analysis/System Biology/Computer Science/ statistics with experience in Machine learning/Al project.
Experience of Deep learning applications in biological data ( image/text).
Proficient in Rf Python machine learning libraries.
Prior experience in the cancer-related project (ML-based) will be advantageous.
Experience with PyTorch/TensorFlow will certainly be very desirable.
Applicant should have strong scientific writing as well as. verbal abilities.
Papers in sci-indexed journals demonstrating ML skill sets.
Database handling will certainly be plus yet not required.

More detail at https://www.aiims.edu/images/pdf/recruitment/advertisement/biochem-16-12-20.pdf

JRF in Bioinformatics @ Central University of Rajasthan

Thu, 20 Aug 2015 05:28:21 -0500

Central University of Rajasthan
Department of Biotechnology
School of Life Sciences
Bandarsindri, Distt. Ajmer

Applications are invited for one JRF position supported by DST sponsored project in Bioinformatics with Dr. Tarun Kumar Bhatt.

Title of the project: Molecular Modeling of malaria parasite ‘secretome’: A potential drug target

Fellowship: Rs. 14000 consolidated

Duration of project: 36 months.

Essential Qualification: Master’s degree in Biotechnology/Bioinformatics with minimum 55% marks. Age limit as per government rule.

Candidates with good experience of molecular modeling, In-silico screening, MD simulation and database formation will be preferred. Good knowledge of Linux operating system is desirable.

How to apply: Interested candidate can send soft copy of application in format given below to tarun@curaj.ac.in on or before 29/08/2015.

1. Name
2. Fathers name
3. Date of Birth
5. Age
6. Sex
7. Address
8. Telephone / mobile no.
9. Email:
10. Academic qualifications starting from 10th class.
11. Summary of experience in molecular modeling, In-silico screening and database formation.

General Conditions:

1.Selected candidate would be informed for date and time of the interview via email .
2. No TA/DA will be paid for attending the interview.

More at http://www.curaj.ac.in/2015/Rec/aug/Advertisement%20for%20post%20of%20JRF%20under%20DST%20project%28BioTech%29.pdf

Bioinformatics Training Fellowship !!

Fri, 28 Aug 2015 16:02:25 -0500

Applications are invited from suitable candidates for six months ‘Training Fellowship’ in Bioinformatics under the BTISNET program of DBT in the Distributed Information Sub center (DISC) facility at NIPGR, New Delhi, under the supervision of Dr. Gitanjali Yadav, Scientist, NIPGR.

Project Title No. of post(s) Designation Stipend in Tenure Start End
Establishment of Distributed Information Sub-Centre (DISC) 02 Trainee Fellow / Student Fellow 5,000/- p.m Six months 01/01/2016 30/06/2016

Essential Qualification:

Traineeship: Candidate having B.Tech or Master Degree or equivalent in Bioinformatics/ Biotechnology with strong interest in Computational Biology and First class/ division throughout academic career may apply.

Studentship: Students currently pursuing the final year of B.Tech or Masters Degree or equivalent in Bioinformatics/ Biotechnology, requiring a thesis as a necessary pre-requisite for completion of respective degree and First class/ division throughout academic career may apply.

Desirable Qualification: Proficiency in Coding Algorithms and Bioinformatics Applications, evidenced by short trainings or computing courses.

The positions are purely temporary and co-terminus with the tenure of the training period as mentioned above. NIPGR reserves the right to select the candidate against the above fellowship depending upon the qualification and experience of the candidate. Reservations shall be as per Govt. of India norms. The applicants will have no claim implicit or explicit for consideration against any regular position of DISC/NIPGR.

Eligible candidates may apply online application form available

at http://www.nipgr.res.in/discform.html within 15 days from the date of

advertisement.Applications received through any other mode will be disqualified outright.

More at http://www.nipgr.res.in/discform.html

Choosing the Right NGS Sequencing Instrument for Your Study

Neel — Wed, 15 Jun 2022 00:37:29 -0500

The right sequencing instrument for your study depends on your project goal. Setting aside turnaround time and price, it essentially comes down to the numbers of reads and read length you need for your experiment. Below, we've described and compared metrics for each of the instruments available. If you’re new to high-throughput sequencing and have questions about how you should design your sequencing run, fill out our free consultation form and we'll get in touch with you to help.

More at https://genohub.com/ngs-instrument-guide/

Address of the bookmark: https://genohub.com/ngs-instrument-guide/

Common steps for reads mapping !

BioStar — Thu, 09 Mar 2023 02:48:02 -0600

Mapping reads to a reference genome is an essential step in many types of genomic analysis, such as variant calling and gene expression analysis. Here are some general steps to follow for mapping reads to a genome:

Choose a read mapper: There are many read mappers available, such as BWA, Bowtie, and HISAT2. Choose a mapper that is appropriate for your type of data and research question.
Index the reference genome: Before mapping reads, the reference genome needs to be indexed. This involves creating an index of the genome sequence that allows the mapper to quickly find matches to the reads. Most mappers have their own indexing tools.
Prepare the read data: The reads should be in a format that is compatible with the mapper. Most mappers accept FASTQ or BAM files. Depending on the quality of the data, it may need to be filtered or trimmed before mapping.
Run the mapper: The mapper is run with the command-line interface or using a graphical user interface. The specific command depends on the mapper being used, but typically involves specifying the input data, reference genome, and output file format.
Evaluate the mapping results: After the mapping is complete, the results should be evaluated. This includes assessing the quality of the mapping, such as the mapping rate, the number of mapped reads, and the mapping quality score.
Post-processing: Depending on the analysis being performed, post-processing of the mapped reads may be necessary. This can include filtering reads based on quality, removing duplicate reads, and calling variants.

Overall, mapping reads to a reference genome is a complex process that requires careful consideration of the type of data, the research question, and the specific mapper being used.

RA Bioinformatics at University of Delhi

Thu, 10 Sep 2015 16:02:37 -0500

BIOINFORMATICS INFRASTRUCTURE FACILITY

GARGI COLLEGE (University of Delhi)

SiriFort Road, New Delhi-110049

Walk- in- interview Bioinformatics Infrastructure Facility (BIF), Gargi College, University of Delhi invites to appear for interview on 29th September, 2015 at 9.30 AM for filling up the following purely temporary position sponsored by DBT, New Delhi.

1. Traineeship – 01 (one post) purely temporary for a period of six months.

Salary: Rs.8000/- p.m. fixed.

Essential Qualification: Post Graduate degree in Bioinformatics or any other branch of Life Sciences preferably with dissertation in Bioinformatics.

Desirable Qualification: Prior knowledge of programming languages such as C, VB, SQL etc. and software/database development.

2. Research Associate-01(one post) purely temporary for a period of nine months.

Salary: Rs 36000/-+HRA p.m fixed.

Essential Qualification: PhD in Bioinformatics/Biological Sciences/Computer Science or allied sciences with proven experience in bioinformatics.

3. Studentship- 01 (one post) purely temporary for a period of six months.

Salary: Rs.8000/- p.m. fixed.

Essential Qualifications: Final year Post Graduate students pursuing a degree in Bioinformatics or any branch of Life Science with knowledge of bioinformatics.

Interested candidates are required to appear for the walk in interview on 29th September, 2015 at 9.30 AM in Principal’s Office, Gargi College, Sirifort Road, N. Delhi-110049, with their CVs, original documents and a set of Photostat copies of all original documents. Conditions: The original documents must be produced at the time of interview, otherwise will not be allowed to attend the same. No TA & DA will be paid for appearing in the interview. The institute reserves the right to fill or not to fill the positions depending upon qualifications/credentials of the candidates etc. The appointment does not confer any right over the job and will not be considered as institute’s service. Dr Aparajita Mohanty Dr Shashi Tyagi (Co-coordinator,BIF) (Coordinator, BIF)

http://gargi.du.ac.in/uploads/ngrey/News/Gargi_Advt_BIF_2015.pdf

List of bioinformatics workflow management tools !

Rahul Nayak — Sat, 20 Mar 2021 00:15:25 -0500

Here are list of Workflow Managers

BigDataScript – A cross-system scripting language for working with big data pipelines in computer systems of different sizes and capabilities. [ paper-2014 | web ]
Bpipe – A small language for defining pipeline stages and linking them together to make pipelines. [ web ]
Common Workflow Language – a specification for describing analysis workflows and tools that are portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments. [ web ]
Cromwell – A Workflow Management System geared towards scientific workflows. [ web ]
Galaxy – a popular open-source, web-based platform for data intensive biomedical research. Has several features, from data analysis to workflow management to visualization tools. [ paper-2018 | web ]
Nextflow (recommended) – A fluent DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner. [ paper-2018 | web ]
Ruffus – Computation Pipeline library for python widely used in science and bioinformatics. [ paper-2010 | web ]
SeqWare – Hadoop Oozie-based workflow system focused on genomics data analysis in cloud environments. [ paper-2010 | web ]
Snakemake – A workflow management system in Python that aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment. [ paper-2018 | web ]
Workflow Descriptor Language – Workflow standard developed by the Broad. [ web ]

National Research Centre on Plant Biotechnology for RA/JRF positions

Sat, 26 Sep 2015 20:32:49 -0500

National Research Centre on Plant Biotechnology - New Delhi, Delhi
National Research Centre on Plant Biotechnology recruitments job vacancies for RA/JRF positions

Name of post: Research Associate
Salary: Rs.36000/-+ 30% HRA*
Educational Qualification: Candidates should have PhD in Biotechnology / Bioinformatics Life Sciences (or) M.Sc Biotechnology / Bioinformatics with three years research experience in relevant field

Name of post: Junior Research Fellow
Salary: Rs.25000/-+ 30% HRA*
Educational Qualification: Candidates should have M.Sc in Biotechnology /Bioinformatics / Life Sciences with 1st Division or 60% marks or equivalent overall grade point from any recognized professional University

Age Limit: 35 years max. (5 years relaxation for SC/ST/OBC)

How to attend walk in interview?
Interested candidates may attend Walk- in-interview on 1st October, 2015 at 10 am at NRCPB, LBS Building, Pusa Campus, and New Delhi-110012 at the above address along with updated Bio-data (CV), ID Proof & attested copies of Certificates and Original to prove qualification & Experience.

Recruitment reference: http://www.nrcpb.org/jobslist

Pacasus: Correction of palindromes in long reads from PacBio and Nanopore

BioStar — Mon, 12 Nov 2018 05:26:48 -0600

Tool for detecting and cleaning PacBio / Nanopore long reads after whole genome amplification. Check the poster from the Revolutionizing Next-Generation Sequencing (2nd edition) conference in the source folder: https://github.com/swarris/Pacasus/blob/master/vib2017.pdf.

The prepint version is found on http://www.biorxiv.org/content/early/2017/08/09/173872

It uses the pyPaSWAS framework for sequence alignment (https://github.com/swarris/pyPaSWAS)

Address of the bookmark: https://github.com/swarris/Pacasus