.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 closing date for application will be 26 June 2015.

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/

Usually when you apply anywhere you need to fulfill some specific kind of requirements which usually include writing a formal application, letter of motivation, research proposal etc. Usually it is hard for grad students to write a crisp, clean and clear letter of motivation. To be honest, you may find several posts on the internet which do tell you how to write professionally. They are good enough to clearly tell you what points should be included, what not and many other things to learn about professional writing. Still, when I look back at my graduation days, I know even after reading many instructions I was not able to write ‘to-the-point’. According to me , writing skill is not something that you can part in binary like- ‘I write perfectly’ or ‘I can not write even a word’. It is something that you learn and get better with the the time. So, I am not going to pin-point the suggestions because you can get it many where but some ‘to-the-point’ things which you may use directly in your letter.

Ideas and main points

Start with writing down some of the main ideas, important points you would like to approach in your letter and later build around them, enrich their content; an example would be :

1. Make your goal clear; provide a short preview of the rest of the letter;
2. Why do you think that the university and the Master's program are interesting and suitable for you? ;
3. Focus on some of your strongest qualifications, past experiences (international experiences are always relevant) and qualities; organise the middle paragraphs in terms of the qualifications most relevant to the programme, you can also refer to your CV for more details;
4. Conclude by restating your interest and show appreciation for the chance to prove yourself in the letter (in some cases you can ask for a personal interview)

How to start-
Your very first line should not be just a line but an impression and reference. None would want to read you unless he knows what it is about. Just like this post. If I would not have written that it is about writing a motivation-letter, you probably would not get annoyed. So start by writing what your letter is about. It could seem like this-

Letter Of Application

Your Address And Contact Details

Receiver’s Address

Dear XYZ

I would like to apply for the…..

or

I am writing here to apply for the…

or

This is regarding your advert. published….

Then Tell Background like-
As my resume reveals, I have Bachelor`s degree from XYZ University and currently, I am…..

Be sure to signify your institution/University like-
I am privileged to obtain my postgraduate education in Bioinformatics at XXX which is known for its enriching academic ambiance where learning and research complement each other.

Then tell about your professional experience like-
Being taught by eminent faculty, I have developed a big interest and passion towards Bioinformatics and managed to have a strong foundation in ……

After that tell how this position would help you, like-
The opportunity to participate in this study would foster….

Assure them that you will make use of whatever you learn there, like-
I plan to ensure the further dissemination of the knowledge and experience gained by this opportunity in…

Close the letter with usual formality, like-
I, hereby enclose a copy of my CV/Resume (whatever it is, there is a difference we all know it) with the hope of consideration. Looking forward to hearing from you.

All the things written above is just my view. You still should see and learn which can be done by one thing and that is -reading about it. Then , please try to write yourself, do not copy /paste. Whatever is written in the post is just to have an idea about the things that should be included in the letter of motivation. You need to write accordingly with a wise choice of words.
Hope this was helpful. You may comment or ask anything if you want to.

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

Dr. Rawal and his US based collaborators have recently secured grant for development of vaccine against an infectious disease agent. For this project, applications are invited for the posts of Junior Research Fellow (two positions) for the following time-bound sponsored projects as per the details given below:

PI: Dr. Kamal Rawal, Biotechnology Department, JIIT, Noida.

Post: JRF (Two)

Job Description: Bioinformatics analysis, Software development, Programming, Text Mining, Deep Curation

Duration: The post is valid upto duration of the project. Continuation is subject to satisfactory performance.

Emoluments depends upon experience and skill sets. We will hire them on following scale:

Junior Scale- Level 1: Rs 22000 per month.

Senior Scale - Level 2: Rs 30000 per month.

Essential Qualification(s) for JRF post:

(A) A Master degree (MSc or MTech or equivalent with minimum of 55% marks) in Bioinformatics/Computer Sciences, IT, Life Sciences, Physical Sciences, Chemical Sciences, Mathematical Sciences or Statistics, Agriculture, Veterinary, Medicine, Pharmacy, Engineering & Technology from a recognized University/Institute and having some experience/skills in bioinformatics, programming, computational or software development work.

(B) In exceptional cases, we can also consider candidates with B. Tech or equivalent with right skill sets and experience for the post of JRFs.

Desirable:

A) Preference will be given to BINC (Bioinformatics National Certification)/DBT-BET/ICMR/ CSIR /UGC/ JRF/ NET qualified candidates. However, Non- NET qualified candidates can also apply.
B) Candidates who have worked with programing, text mining, NGS data analysis etc are encouraged to apply.
Updated resume including a cover letter (preferably by E. mail) should be mailed to bioinfocvatgmaildotcom, and Dr. Kamal Rawal at kamaldotrawalatgmaildotcom. Short listed candidates would be called for interview. No TA/DA will be paid to the candidates called for interview.

Candidate may also fill the following form:

https://docs.google.com/…/1FAIpQLSdZoZ21ZoNRStEeL5…/viewform

Or

http://tinyurl.com/bioinfocv2017

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

http://statbio.github.io

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/

Address of the bookmark: https://bioconda.github.io/recipes/snakemake/README.html