This workflow includes the following tools which are needed to be installed in the system.

1. fastp
2. spades assembler
3. QUAST
4. bwa
5. samtools
6. metabat2
7. CheckM

Address of the bookmark: https://github.com/avishekdutta14/iMAGine

Translational recoding.

RNA editing.

Evolution of the genetic code and translation.

More at http://lapti.ucc.ie/research.html

Lab page http://lapti.ucc.ie/index.html

Address of the bookmark: http://www.mdpi.com/2073-4425/3/3/423

Name of the fellowship: Junior Research Fellow (JRF) / Project Fellow

Title of the project: Genome-wide Mapping of Murine Specific Dengue T-cell Epitopes: Computational Prediction, Identification and use as Candidate Vaccines

Duration: 3 years

Fellowship: Rs. 18,000 for first 2 years and Rs. 20,000 for 3rdyear (for M.Tech. candidates)

Rs. 16,000 for first 2 years and Rs. 18,000 for 3rdyear (for M.Sc. candidates with NET qualification)

Rs. 8,000 for first 2 years and Rs. 10,000 for 3rdyear (for M.Sc. candidates without NET qualification)

Qualifications: M.Tech. in Biotechnology / M.Sc. in any branch of Life Sciences

Desirable Experience: Minimum of two years research experience in any of the following areas: Immunology / Microbiology / Gene Manipulation / Bioinformatics

Interested and eligible candidates may apply with their resume along with relevant documents and a passport size photograph to the Principal Investigator by post (or e-mail) on or before December 31, 2013. Only short listed candidates will be called for written test and/or interview. Selected candidate may register for PhD in Kalasalingam University. No TA/DA will be paid for attending interview.

Dr. K. Sundar
Principal Investigator (SERB Project)
Department of Biotechnology
Kalasalingam University
Krishnankoil – 626126, Tamil Nadu
sundarkr@klu.ac.in

Established by Government of Rajasthan

Approved by UGC under Sec 2(f) of UGC Act 1956

ADVERTISEMENT FOR FACULTY POSITION AT JAIPUR NATIONAL UNIVERSITY,JAIPUR

Jaipur National University, Jaipur is a premier centre of learning, providing various integrated and interdisciplinary programmes of study and research in the country. With the opening of the School of Distance Education & Learning, JNU has taken education to the doorsteps of those aspirants who, for some reason, could not be a part of regular stream of education. In this era of competition & ambition for excellence, it has become imperative to have quality education & an alert mind coupled with the right attitude to carry onself, and for this, JNU happens to be the most sought after destination.

School Of Life Sciences: Bioinformatics, Chemistry

Total no of Post: 04

Education:

PG – M.Sc /M.Tech Bioinformatics

PG – M.Sc /M.Tech Chemistry

Experience:

Candidate with 1-2 years of teaching experience in college/ University will be preffered. Freshers may also apply.

Compensation: Compensation will not be a problem for the right candidate

HOW TO APPLY:

SEND THE UPDATED RESUME THROUGH MAIL OR POST AT

dsbhatia5@yahoo.com

contact no: 7568246839

Website: http://www.jnujaipur.ac.in

Please mail your resume to Prof.D.S.Bhatia

Email Address: dsbhatia5@yahoo.com

Ph:, +917568246839

.NET Bio

http://blogs.msdn.com/b/msr_er/archive/2011/10/18/microsoft-biology-foundation-evolves-into-new-toolkit-net-bio.aspx

A language-neutral bioinformatics toolkit built using the Microsoft 4.0 .NET Framework to help developers, researchers, and scientists.

AMPHORA ("AutoMated Phylogenomic infeRence Application")

http://wolbachia.biology.virginia.edu/WuLab/Software.html

Metagenomics analysis software

Anduril

http://www.anduril.org/anduril/site/

Component-based workflow framework for data analysis

Armadillo workflow platform

Tool for designing and executing phylogenetic workflows

AutoDock

http://autodock.scripps.edu/

suite of automated docking tools

Biochemical Algorithms Library (BALL)

http://www.ball-project.org/

C++ library and framework for molecular modeling and visualization designed for rapid prototyping

Bio4j

http://bio4j.com/

Bio4j is a bioinformatics platform and graph based database built around most data available in UniProt KB(Swiss-Prot + TrEMBL), Gene Ontology (GO), UniRef (50,90,100), RefSeq, NCBI taxonomy, and Expasy Enzyme DB

Bioclipse

www.bioclipse.net

Visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP).

Bioconductor

http://www.bioconductor.org/

R (programming language) language toolkit

Bioinformatics Learning Tutorial (BLT)

http://sourceforge.net/projects/biotutorial/

Educational interactive tutorials and 3D animations for Replication, Transcription, and Translation

BioHaskell

http://biohaskell.org/

Haskell (programming language)

BioJava

http://biojava.org/wiki/Main_Page

Java (programming language)

BioMOBY

http://biomoby.org/

registry of web services

BioPerl

http://www.bioperl.org/wiki/Main_Page

Perl language toolkit

BioPHP

http://www.biophp.org/

PHP language toolkit

Biopython

http://biopython.org/wiki/Main_Page

Python language toolkit

BioRails

https://github.com/biorails

a data management system designed to support researchers in drug discovery

BioRuby

http://bioruby.org/

Ruby language toolkit

BioSmalltalk

https://code.google.com/p/biosmalltalk/

Smalltalk language toolkit

BioUno

http://www.biouno.org/

BioUno is a project that applies Continuous Integration tools and techniques in Bioinformatics. It uses Jenkins and its plug-in API to create biology workflows and manage computer clusters.

caCORE

ontologic representation environment

caArray

https://cabig-stage.nci.nih.gov/community/tools/caArray

ontologic representation environment

EMBOSS

http://emboss.sourceforge.net/

Suite of packages for sequencing, searching, etc.

Gaggle

https://www.gaggle.net/

A framework for interoperability between systems biology software

Galaxy

http://galaxyproject.org/

Scientific workflow and data integration system

GenePattern

http://www.broadinstitute.org/cancer/software/genepattern/

Scientific workflow system that provides access to more than 150 genomic analysis tools

GeWorkbench

http://wiki.c2b2.columbia.edu/workbench/index.php/Home

Genomic data integration platform

GMOD

http://www.gmod.org/wiki/Main_Page

Toolkit for addressing many common challenges at biological databases.

GeneProf

http://www.geneprof.org/GeneProf/

A web-based, bioinformatics software suite for the analysis of functional genomics experiments, e.g. RNA-seq or ChIP-seq.

GeneTalk

http://www.gene-talk.de/

Tool for filtering sequence variants in VCF files. Network for scientists and clinicians for expertise and knowledge exchange. Database of annotations aboute sequence variants with clinically relevant information.

GenGIS

http://kiwi.cs.dal.ca/GenGIS/Main_Page

Application that allows users to combine digital map data with information about biological sequences collected from the environment.

GenomeSpace

http://www.genomespace.org/

Centralized web application that provides data format transformations and facilitates connections with other bioinformatics tools

GENtle

http://directory.fsf.org/wiki/GENtle

An equivalent to the proprietary Vector NTI, a tool to analyze and edit DNA sequence files

Integrated Genome Browser

http://bioviz.org/igb/

Java-based desktop genome browser

Integrative Genomics Viewer (IGV)

http://www.broadinstitute.org/igv/

High-performance desktop tool for interactive visual exploration of diverse genomic data

IntAct

http://www.ebi.ac.uk/intact/

molecular interaction database

InterMine

http://intermine.github.io/intermine.org/

Extensive data warehouse system for the analysis and integration of biological datasets

Java Treeview

http://jtreeview.sourceforge.net/

microarray data viewer

LabKey Server

http://labkey.com/

platform for integrating, analyzing and sharing data

OpenClinica

https://www.openclinica.com/

software for capturing and managing data in clinical trials

PromKappa

http://xbioinformatics.wordpress.com/tag/promkappa/

PromKappa (Promoter analysis by Kappa) software program used for promoter pattern generation and promoter analysis.

MeV: Multi-Experiment Viewer

http://www.tm4.org/mev.html

a desktop application for the analysis, visualization and data-mining of large-scale genomic data

PathVisio

http://www.pathvisio.org/

a desktop software for drawing, analysis and visualization of biological pathways

REDCRAFT

software for determining tertiary protein structure given assigned Residual Dipolar Coupling data

SAM Tools

Data format (SAM) and accompanying tool suite, for storing large nucleotide sequence alignments

Staden Package

Sequence assembly, editing and analysis, primarily consisting of gap4, gap5 and spin.

STAMP

Software package for analyzing metagenomic profiles that promotes ‘best practices’ in choosing appropriate statistical techniques and reporting results.

supraHex

An open-source R/Bioconductor package for omics data analysis using a supra-hexagonal map

Taverna workbench

Tool for designing and executing workflows

TGAC Browser

Genome Browser, visualisation solutions for big data in the genomic era

T-REX WebServer

Bioinformatics and phylogenetics webserver (NJ, PhyML, RAxML, MAFFT, MUSCLE, Newick viewer, Horizontal gene transfer detection, Reticulograms, Substitution models)

UGENE

integrated bioinformatics tools

Visomics

bioinformatics tools for omics data

Genome Analysis Toolkit 1.0 (GATK 1.0)

a software package to analyse next-generation resequencing data

The 2014 CeMM PhD Program will focus on two thematic areas: INFECTION and CANCER, that are built on the pillars of epigenetics, bioinformatics and systems biology, chemical biology and the mechanism of action of drugs, high-throughput genetics, genomics and proteomics, and molecular and cell biology.

The choice of this strategic focus rests on the synergies between immunology, infection and cancer in pathophysiological and technological terms. It furthermore reflects the strength of the current CeMM faculty, itself built around the historical and contemporary expertise in immunology and cancer of the Medical University of Vienna.

As a CeMM PhD student you will get the chance to work at the cutting edge of interdisciplinary molecular medicine research and be trained by the entire CeMM and associated faculty to become one of the scientists shaping the future of molecular medicine.
Requirements

To be eligible to enroll in the CeMM PhD Program all candidates are required to have a bachelor’s or master’s degree in medicine, biology, chemistry, bioinformatics, mathematics or any scientific/technical, subject-relevant degree. Candidates do not need to have completed their degree at the time of application, however they must have obtained their final degree certificate by mid-September. The working language at CeMM is English, so excellent written and oral communication skills in English are required.
Timeline

Applications open on 20th January and close on 20th March 2014.
Two references are required to be submitted through the online system by 31st March 2014.
All complete candidate applications are reviewed by the CeMM Faculty in early April.
Selected candidates are invited to a Skype panel interview in late April.
Shortlisted candidates are then invited to Vienna in May for a full interview process, including an opportunity to introduce yourself through a presentation and interview rounds, meet research group members, and attend an informal dinner to get to know the Faculty members and learn more about their research.
Positions are offered by CeMM Faculty in June.
Start of PhD Program: 1st October 2014 .

Contact

Binia Maria Günther, BEd BA
Human Resources Manager
bguenther@cemm.oeaw.ac.at

Catherine Lloyd, Ph.D.
PhD and Postdoc Program Manager
clloyd@cemm.oeaw.ac.at

More Info: www.cemm.oeaw.ac.at/phd-program/application/

No. CSE/14/1038

Walk in Interview for the post of JRF under TEQIP-II

SN Department – Qualification Post Graduation – Time

1 Bio-Informatics & Mathematics M.Tech Bio-informatics/M.Sc.* Maths 10.00 AM

2 Biological Sciences M.Sc.* in any branch of Biological Sciences 10.30 AM

3 Chemical Engineering M.Tech Chemical Engineering 11.00 AM

4 Chemistry M.Sc.* Chemistry 11.30 AM

5 Civil Engineering M.Tech Structure/GeoTech. /Water -Resources/Hydraulics/Environment/Transport 12.00 Noon

6 GIS M.Tech GIS/Civil 12.30 PM

7 Computer Science & Engineering M.Tech CSE/Information Security 01.00 PM

8 Electrical Engineering M.Tech Electrical Derives 01.30 PM

9 Electronics & Communication M.Tech Digital Communication 02.00 PM

10 MSME M.Tech Material Science/ Mechanical/Metallurgy 02.30 PM

11 Physics M.Sc.* Physics 03.00 PM

* M.Sc. with NET/GATE qualified

Resume along with one passport size photograph and relevant documents are required at the time of interview

Amount of Fellowship: Rs 18000/-month+ HRA

Duration: 31st Dec 2014 (End of TEQIP-II project)

Date of Interview: 7th February 2014

Venue Institute Committee Room

Advertisement:

http://www.manit.ac.in/manitbhopal/Year2014/Recruitment/Advertisement%20JRF.pdf

Qualifications

PhD or Post-Graduated Master degree is required. Successful candidates will have some expertise in data analysis of NGS data by using methods running in R and UNIX environment. Familiarity with genome databases and browsers is required.

Application

Candidates should send a CV and a brief personal statement focusing on their skills and interests related to the research project.

Contacts

Start date: 1° April 2014
Salary on grant: 25,000 euros per year.
Contact Person (Referent): Mario Capasso
Ref. Email: mario.capasso@unina.it and achille.iolascon@unina.it
Tel: +39 081 3737889

If you have a license key for Modeller 8 or 9, there is no need to reregister for Modeller 9.13 - the same license key will work. (It won't do any harm to reregister if you want to, though!)

9.13 is primarily a bugfix release relative to the last public release(9.12). Major user-visible changes include:

# Modeller now includes a variety of SOAP (statistically optimized atomic potential) scores for assessing proteins, loops, and interfaces.

# The Lennard-Jones interaction energy is now artificially truncated at very short distance; this makes simulations with poor starting conditions much less likely to 'blow up'.

# model.get_insertions(), model.get_deletions() and model.loops() now have an include_termini option; if False, residue ranges that include chain termini are excluded from the output.

See the Modeller manual for a full change log: http://salilab.org/modeller/9.13/manual/node39.html

If you encounter bugs in Modeller 9.13, please see http://salilab.org/modeller/9.13/manual/node10.html for information on how to report them.

Reference:

http://salilab.org/modeller/