https://gist.github.com/santhilalsubhash/367befcf5216be4b1fd9

Information:

This script converts EnsEMBL GTF (Ex: https://gist.githubusercontent.com/santhilalsubhash/1e7cca357e52a181dc25/raw/cfb803e07900a2baefbb6534f1299fd30cb57a29/sample.GTF) file to annotation table format. It generated two files
1) Transcript wise chromosome location with information about transcripts (Ex: https://gist.githubusercontent.com/santhilalsubhash/c7dec516e0338503a4b6/raw/de0af1a39f0005c4ce7321c5ae57fc8b4a14c7f4/sample.GTF_enst_annotation.txt)
2) Gene wise chromosome location with information about genes (Ex: https://gist.githubusercontent.com/santhilalsubhash/c92006c5080f0333bec2/raw/d16e0b2440d73b09b486d3c9751cdb248a73fa0b/sample.GTF_ensg_annotation.txt)

Note: You can download GTF files from http://www.ensembl.org/info/data/ftp/index.html

1. Work to establish improved quantitative experimental assays (such as microarrays or differential in-gel electrophoresis) and
2. Development of modern computational methods (such as hierarchical probabilistic models or integration of heterogeneous data sources)

Lab page @ http://bioinf.boku.ac.at/

Free Bioinformatics workbench https://www.mn.uio.no/ifi/english/research/networks/clsi/earlier_seminars/2012/tammivesth_osloseminarfinal.pdf

Please add ur links/bookmarks in comment section.

Address of the bookmark: http://physicsdatabase.com/free-math-books/

Address of the bookmark: https://github.com/dhlbh/BASE

Address of the bookmark: http://bioinformatics.oxfordjournals.org/content/23/14/1713.full

usage:   canu [-correct | -trim | -assemble | -trim-assemble] \
              [-s ] \
               -p  \
               -d  \
               genomeSize=[g|m|k] \
               -maxThreads=2 \
               useGrid=false \
              [other-options] \
               read_file.fastq.gz

A default Canu run produces usually high quality assembly, example of a command that was used for testing can be found below. However, there are still a lot of parameters that are possible to tweak. For example if we desire to assemble haplotypes separately of if we want to smash them together, we can alternate the error correction process.

canu -p test_asmbl \
     -d asm_test3 \
     genomeSize=2m \
     -maxThreads=2 useGrid=false \
     -pacbio-raw \ ~/pacbio/dna/sample_reads.fastq.gz

There is a brilliant section in documentation about parameter tweaking.

The output directory contains will contain many files. The most interesting ones are:

• *.correctedReads.fasta.gz : file containing the input sequences after correction, trim and split based on consensus evidence.
• *.trimmedReads.fastq : file containing the sequences after correction and final trimming
• *.layout : file containing informations about read inclusion in the final assembly
• *.gfa : file containing the assembly graph by Canu
• *.contigs.fasta : file containing everything that could be assembled and is part of the primary assembly

The basic stats of assembly can be read from reports generated by the assembler, or calculated using standard UNIX command line tools.

More at https://canu.readthedocs.io/en/latest/faq.html

CENTRE FOR BIOINFORMATICS

PUDUCHERRY

Applications are invited for one Project Assistant to work in the UGC sponsored Research Award "Molecular Docking and Dynamics studies to understand the interacting mechanism of oncogenic 101 protein with its cellular proteins".

The duration for the fellowship is 12months only with consolidated pay ofRs. 5,000 per month.

Application on plain paper with following details: Name, Address, Data of Birth, Father's Name, Nationality, Educational Qualification (SSLC onwards-enclose attested copies of certificate) and Researcb Experience may be addressed to Dr. R. Krishna, Principle Investigator (PI), UGC Research Award, Centre for Bioinformatics, Pondicherry University, Pondicherry - 605 014.

Application should reach in January 261h , 2013.

Essential Qualification: M.Sc. in Bioinformatics/Biophysics with good academic record.

Qualification for Project Fellow:

M.Sc in Bioinformatics/Biophysics.

The person to be considered for appointment as Project Fellow must have second class master degree with a minimum of 55% marks in the subject concerned or a related subject.

The candidate to be appointed as Project Fellows should be below thc age of40 years at the time of appointment.

Desirable Qualification for this Project: Research Experience in Small/Macromolecule Crystallography and Structural Bioinformatics.

For more details, refer the web site: www.pondiuni.edu.in/sites/default/files/BIC-311213.pdf

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

(Under Tenure-Track Model)

Open Advt. No IIITA/DIC/16012014

IIIT-Allahabad has several Openings for the Faculty positions at the Assistant Professor level.

It is a regular tenure-track faculty positions for 3-5 years in teaching and research. A regular faculty is expected to engage heavily in research and teaching. The eligibility criteria for regular faculty positions are similar as in IITs. For an Assistant Professor position, a candidate must have a PhD (in IT/Computer Science &/or Engineering/Electrical, Electronics &/or Communication Engineering/etc; for interdisciplinary areas the PhD may be in an appropriate field), plus three years experience. However, for PhDs from a well known University/Institute (e.g. IITs/IISc/TIFR/ISI in India or well known research universities across the world), and a good research/academic record, the 3 years experience requirement may be waived.

The pay scale for faculty is same as in IITs. Other benefits include initiation research grant, travel support, book grant, professional society membership, etc., and personal benefits such as medical/LTC, on campus subsidized family housing with excellent modern infrastructural facilities.

Areas of Interest

IIIT-Allahabad aims to build strong research groups in important and emerging areas in CS/IT/ECE as well as in emerging interdisciplinary areas, and applications are invited in all these areas. Some of the areas of special interest, besides strengthening the existing research areas, are : Software Engineering, Theoretical Computer Science, Cyber Physical Systems, Robotics, Network science, Digital Media, Computational neuroscience, Machine learning, Healthcare informatics, Computational Biology, Communications networks (both at hardware and protocol levels), Circuits (including VLSI, analog, low power, etc), Energy systems and technologies, Biomedical electronics and systems, Computer Architecture, signal/image processing, Embedded and control systems.

Application Process

Interested candidates can apply by sending their detailed CV with list of publications clearly mentioning Journal names and citation index with three references through email entitled “Faculty positions at IIIT Allahabad” to faculty.applications@iiita.ac.in. Do not send your applications in any other email addresses. Applications will be considered regularly, hence there is no deadline for applying.

Important Clarifications on Eligibility

A PhD in CS/IT (or other disciplines, as announced) is the minimum expected requirement for an Assistant Professor.

Advertisement: http://iiita.ac.in/pub/Faculty-Position-IIITA1.pdf