1.automatic learning of chemical reactivity and metabolism,
2.simulation of NMR spectra,
3.modelling of properties of ionic liquids, and
4.representation of molecular chirality.

More at http://joao.airesdesousa.com/

Basic Galaxy Tutorial

• RNA-Seq tutorial based on Trapnell et al. (2012) Nature Protocols

In this tutorial we cover the concepts of RNA-Seq differential gene expression (DGE) analysis using a very small synthetic dataset from a well studied organism.

Advanced Galaxy Tutorial

• RNA-Seq (Advanced) Tutorial

In this tutorial we compare the performance of three statistically-based differential expression tools:

* CuffDiff

* EdgeR

* DESeq2

Advanced Command Line Tutorial

• Graphical Output with CummeRbund introduces some basic commands using the cummeRbund package of the R programming language

You will need to install R, RStudio and cummeRbund on your PC (explained in the Tutorial). You will learn how to produce graphical output from RNA-Seq analysis previously done using a Cuffdiff analysis.

Variant Detection

Basic Galaxy Tutorial

• Variant Detection tutorial

In this tutorial we cover the concepts of detecting small variants (SNVs and indels) in human genomic DNA using a small set of reads from chromosome 22.

Advanced Galaxy Tutorial

• Variant Detection (Advanced) Tutorial

In this tutorial we compare the performance of three statistically-based variant detection tools:

* SAMtools: Mpileup

* GATK: Unified Genotyper

* FreeBayes

Each of these tools takes as its input a BAM file of aligned reads and generates a list of likely variants in VCF format

Pipelines are for those who are comfortable with using the UNIX command line; and often allow more control over branching and iteration logic.

• WGS/exome GATK-based variant calling pipeline

This is a basic variant-calling and annotation pipeline developed at the Victorian Life Sciences Computation Initiative (VLSCI), University of Melbourne. It is based around BWA, GATK and ENSEMBL and was originally designed for human (or similar) data. The master branch is configured for WGS data; there is an exome branch configured for variant calling in exome data.

To run the pipeline you will need Rubra: https://github.com/bjpop/rubra. Rubra uses the python Ruffus library: http://www.ruffus.org.uk/.

Protocols

• Familial Variant Calling

In this protocol we discuss and outline the process of calling familial related mutations.

• Somatic Variant Calling

In this protocol we discuss and outline the process of identifying somatic variants or mutations.

Assembly

Basic Galaxy Tutorial

• Genome assembly tutorial

In this tutorial we carry out de novo assembly of a microbial genome. We have also written a De novo Genome Assembly for Illumina Data Protocol for a more generic description of the method.

Protocol

• De novo Genome Assembly for Illumina Data

In this protocol we discuss and outline the process of de novo assembly for small to medium sized genomes. Use our Genome assembly tutorial to learn a specific case of using Galaxy to carry out de novo assembly of a microbial genome.

Small RNAs

Basic Galaxy Tutorial

• Quality control for small RNA

This tutorial covers initial steps of the workflow for analysis of short RNA expression such as a quality control of the raw reads, processing of the raw reads for the subsequent analysis and initial quality assessment of the library.

ChIP Seq

Protocol

• ChIP-Seq

In this protocol we discuss ChIP-Seq: a method to analyze the interaction between proteins and DNA.

Amplicons

Protocol

• Amplicon Alignment

In this protocol we discuss and outline the process of aligning custom amplicons using primers for high precision.

Learn Galaxy

Introduction to Galaxy, for those who are very new to Galaxy.

Using Histories and Workflows, for those with some Galaxy knowledge.

The Galaxy project website has many tutorials and screencasts about using Galaxy and the tools, and developing new tools.

Address of the bookmark: https://genome.edu.au/wiki/Learn

The work will focus on the functional studies of small RNAs by using next-generation sequencing approaches.

Candidates should hold a Ph.D. degree and have strong background in bioinformatics.
The University of Nice Sophia-Antipolis provides a wide range of facilities and training essential for biomedical research.

Interested applicants should send a PDF with a cover letter stating research interests and qualifications, an updated CV, a summary of previous research experience and contact information for two references to Michele Trabucchi ( mtrabucchi@unice.fr )

Homepage: http://www.unice.fr/c3m/EN/Equipe10.html

The Bioinformatics and Systems Biology Unit of Université de Liège (Belgium) is looking for a highly motivated master student with programming skills for a PhD thesis project (4 years, fully funded) with the goal of designing computational tools that use literature, genomic and structural data in order to infer regulatory and metabolic networks.

Applicants are invited to send their resume and a recommendation letter to Prof. Patrick Meyer (more details at www.biosys.ulg.ac.be )

For more information : www.biosys.ulg.ac.be

01. Scientist II 01
Essential: Ph.D. degree in Life Sciences from a recognized university along with a minimum of 2 years of research experience in Bioinformatics as evidenced by publications in the peer reviewed journals.

OR
Ph.D. degree in Bioinformatics from a recognized university.

OR
M.Sc. in Bioinformatics from a recognized university along with a minimum of 3 years of research experience in Bioinformatics as evidenced by publications in the peer reviewed journals.

Desirable:
Thorough Knowledge about In silico genome analysis and comparative genomics.
Experience with in silico identification of novel virulence factors of pathogens, host-pathogen interactions and Systems Biology.
Additional Postdoctoral research experience in relevant subjects from a recognized institutions.

Rs. 44,000/- p.m. (consolidated) plus 30% HRA

Below 40 years

Applications along with Bio-Data containing detail work experience and full list of publications may be sent via email tosantasabujdas@yahoo.com latest by October 27, 2014.

Short-listed candidates will be called via email for an interview to be held at the institute in the second week of November, 2014.

Advertisement: www.niced.org.in/placements.htm

Details are available at www.nehu.ac.in and www.bicnehu.ac.in.

Applications must reach the undersigned within 15 days from the date of publication of this advertisement.

Prof. Pramod Tandon. PI/Mr. Devendra Kumar Biswal (Co-PI)

Detail tutorial at https://janggu.readthedocs.io/en/latest/

USE cases

https://github.com/wkopp/janggu_usecases

Address of the bookmark: https://github.com/BIMSBbioinfo/janggu

• Expansion of Protists and Fungi with hundreds of annotated genomes
• Variation data for bread wheat, rice, Aedes aegypti, and Ixodes scapularis
• Whole genome alignments for O. longistaminata and T. cacao
• Non-coding RNA gene models in Bacteria
• New assembly of tomato (version 2.50)
• Full support for UCSC Track Hub format for hosting your own data in Ensembl

More at http://www.ensembl.info/blog/2015/06/16/ensembl-genomes-release-27-is-out/

The main features are, it supports many standard file formats such as GFF, BED, GTF, FASTA, VCF, BAM and it can be integrated with other browsers or tools for analysis of genome.