Abstract: Strand NGS supports an extensive workflow for the analysis and visualization of RNA-Seq data. The workflow includes Transcriptome / Genome alignment, Differential expression analysis with Statistical approach and Splicing events detection. Strand NGS also supports novel discovery like identification of novel genes, exons and Novel splice junctions, alongside it can also detect gene fusion events. Further downstream analysis such as GO and pathway analysis can be performed on the set of interesting genes. The product has an option to create pipelines for time consuming jobs which automates analysis and leaves more time for end data interpretation. This webinar will give an overview of the features in the RNA-Seq data analysis workflow in Strand NGS and also highlights on parameters within each feature that can be optimized depending on datasets and analysis needs.

Speaker: Mr. Sugandan Sivamani, Senior Application Scientist, Strand Life Sciences

Date: 9th Nov, Session 1 for SAPK/ APFO: 2:30 PM IST Date: 9th Nov, Session 2 for AFO/ EMEA: 9:00 AM PST

Register here http://www.strand-ngs.com/webinar_registration

Grinder can produce genomic, metagenomic, transcriptomic, metatranscriptomic, proteomic, metaproteomic shotgun and amplicon datasets from current sequencing technologies such as Sanger, 454, Illumina. These simulated datasets can be used to test the accuracy of bioinformatic tools under specific hypothesis, e.g. with or without sequencing errors, or with low or high community diversity. Grinder may also be used to help decide between alternative sequencing methods for a sequence-based project, e.g. should the library be paired-end or not, how many reads should be sequenced.

Address of the bookmark: https://sourceforge.net/projects/biogrinder/files/biogrinder/

Input

Jabba takes as input a concatenated de Bruijn graph and a set of sequences:

the de Bruijn graph should appear in fasta format with 1 entry per node, the meta information should be in the format:
>NODE
the set of sequences should be in fasta or fastq format. These sequences will be corrected (e.g. PacBio reads). The corrections will be written to a file Jabba fasta.
The output is a file in fasta format with corrections of the long reads, and additionally a file in the input format containing uncorrected reads.

https://github.com/biointec/jabba/wiki

https://almob.biomedcentral.com/articles/10.1186/s13015-016-0075-7

Address of the bookmark: https://github.com/biointec/jabba

Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools.

Commonly used biological software and example script files for different assembly pipelines have also been provided, where the example script files can be updated to suit one’s experimental needs. Genobuntu attempts to reduce the amount of time and energy needed to build software workstations and it can also act as a good teaching source for a class room setting.

Therefore, Genobuntu offers a well-tailored environment for both novices and experts working in the field of genome assembly.

Address of the bookmark: https://sourceforge.net/projects/genobuntu/

Link for those who looking for structure of Bam and sff file:

Bam:

http://samtools.sourceforge.net/SAMv1.pdf (from page 12)

sff file (for Ion torrent and 454 files):

http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=format#sff

Binary file Editor and Viewer:

http://mh-nexus.de/en/hxd/

http://www.isb-sib.ch/education/training-courses.html

Canadian bioinformatics also organises various bioinformatics and sequencing courses:

http://bioinformatics.ca/workshops

In addition to above two, EMBI Europe, EMBO Europe, Cold Spring Harbour USA, Wellcome Trust UK and NOVA Europe also organise bioinformatics and sequencing courses annually:

http://www.embl.de/training/events/index.php?p_outstation=ALL

http://www.embo.org/funding-awards/courses-workshops

http://meetings.cshl.edu/courses.html

http://www.wellcome.ac.uk/Education-resources/Courses-and-conferences/Advanced-Courses-and-Scientific-Conferences/Advanced-Courses/index.htm

http://www.nova-university.org/pagetop.cfm?MenySidorTop_id=2&open=7

Dan Kortschak, Bioinformatics Group, School of Molecular and Biomedical Science ,The University of Adelaide

Address of the bookmark: http://talks.biogo.googlecode.com/git/illumination/illumination.pdf

The biggest and perhaps most fearsome of the world's big cats, the tiger, shares 95.6 percent of its DNA with humans' cute and furry companions, domestic cats.

The new research showed that big cats have genetic mutations that enabled them to be carnivores. The team also identified mutations that allow snow leopards to thrive at high altitudes.

Reference:

http://www.nbcnews.com/science/your-cat-ferocious-tigers-share-lot-95-6-percent-their-4B11182690

http://timesofindia.indiatimes.com/home/environment/flora-fauna/Gene-mapping-of-tiger-completed/articleshow/22671681.cms

Paper:

http://www.nature.com/ncomms/2013/130917/ncomms3433/full/ncomms3433.html

"In neuroscience, the project will use neuroinformatics and brain simulation to collect and integrate experimental data, identifying and filling gaps in our knowledge, and prioritising future experiments.

In medicine, the HBP will use medical informatics to identify biological signatures of brain disease, allowing diagnosis at an early stage, before the disease has done irreversible damage, and enabling personalized treatment, adapted to the needs of individual patients. Better diagnosis, combined with disease and drug simulation, will accelerate the discovery of new treatments, drastically lowering the cost of drug discovery.

In computing, new techniques of interactive supercomputing, driven by the needs of brain simulation, will impact a vast range of industries. Devices and systems, modelled after the brain, will overcome fundamental limits on the energy-efficiency, reliability and programmability of current technologies, clearing the road for systems with brain-like intelligence."

Source: http://www.forbes.com/sites/jenniferhicks/2013/10/07/the-human-brain-project-begins/ 

(https://www.facebook.com/humanbrainproj/info)

Home Page:

https://www.humanbrainproject.eu/

Jobs:

https://www.humanbrainproject.eu/participate/jobs

Address of the bookmark: http://grouthbio.com/Genome_Software_Service.php