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ISB’s 2012 Annual Report is Now Online

ISB’s 2012 Annual Report is Now Online | Bioinformatics Training | Scoop.it
 
ISB’s annual report is now available. This year, we created a web site for the report. It highlights nine headlines from 2012 and also includes a stirring piece from our president, Dr.
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Bioinformatics Training
Bioinformatics, blended with education and health sciences subjects
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GTPB: CSDM14: Chromosome structure determination using modelling and Hi-C data

GTPB: CSDM14: Chromosome structure determination using modelling and Hi-C data | Bioinformatics Training | Scoop.it

The sequence of a genome alone does not carry enough information to fully understand how genomic processes are carried out in the cell nucleus; to achieve this, the knowledge of the three-dimensional (3D) architecture of a genome is necessary. Advances in genomic technologies and the development of new analytical methods, such as 3C-based methods, have allowed getting insights at unprecedented resolution into how the genome is organized. Recently, it has been shown that chromatin is organized in Topologically Associating Domains (TADs), large interaction domains that appear to be conserved among different cell types. In this course, participants will learn to use TADbit, a software for the analysis and modeling of Hi-C data.

The course will cover all the aspect of modeling with Hi-C data:

Generation of Hi-C contact matrices from raw data (that is, iterative mapping of the fastq reads to the reference genome, cleaning and normalization)Analysis of Hi-C matrices (Hi-C map visualization, TAD identification, experiment comparison, and TAD selection)3D modeling and analysis of TADs

The 3D module of TADbit is based on a computational module of the Integrative Modeling Platform (IMP, http://www.integrativemodeling.org) that uses chromosome conformation capture data to determine the 3D architecture of genomic domains and entire genomes at unprecedented resolutions. Participants can bring-in specific biological questions and/or their on data to work on during the course. At the end of the course, participants will be familiar with the TADbit software, enabling them to fully analyze and model Hi-C data.

Pedro Fernandes's insight:

How to use Hi-C data in probing for genome structure, build your own  skills to use the TADbit software.

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Cancer Genomics Cloud: ISB and Google Featured in MIT Tech Review

Cancer Genomics Cloud: ISB and Google Featured in MIT Tech Review | Bioinformatics Training | Scoop.it
(Above illustration from MIT Technology Review.)
MIT Technology Review published an article about the launch of Google Genomics and included a mention of ISB’s new Cancer Genomics Cloud project.
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Center for Data Innovation » Tool Lets Bioinformatics Researchers Explore Data on the Fly

Center for Data Innovation » Tool Lets Bioinformatics Researchers Explore Data on the Fly | Bioinformatics Training | Scoop.it
Tool Lets Bioinformatics Researchers Explore Data on the Fly http://t.co/ShgqSQE6cS via @datainnovation

Via HaBIc
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Real Simple Magazine Quotes ISB on ‘What Exactly is Wellness?’

Real Simple Magazine Quotes ISB on ‘What Exactly is Wellness?’ | Bioinformatics Training | Scoop.it
Above: Cover of the November 2014 issue of Real Simple Magazine
A team at ISB has been working on the 100K Wellness Project, which you read about here. The November issue of Real Simple Magazine has a feature story on “What Exactly is Wellness?
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Baliga Lab: Uncovering the Genetic Adaptability of Tuberculosis

Baliga Lab: Uncovering the Genetic Adaptability of Tuberculosis | Bioinformatics Training | Scoop.it
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The Institute for Systems Biology and Seattle BioMed have collaborated to reconstruct the gene regulatory network of the human pathogen Mycobacterium tuberculosis.
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ISB 2014 Retreat

ISB 2014 Retreat | Bioinformatics Training | Scoop.it
ISB held its all-staff retreat in Leavenworth on Sept. 8 and 9. In order to do the kind of science we do, we need time away to connect with one another, recharge and envision big ideas.
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ISB Gets $6.5 Million From NCI to Create ‘Cancer Genomics Cloud’ with Partners Google and SRA International

ISB Gets $6.5 Million From NCI to Create ‘Cancer Genomics Cloud’ with Partners Google and SRA International | Bioinformatics Training | Scoop.it
PRESS RELEASE Institute for Systems Biology (ISB) has received a $6.5 million two-year contract from the NIH’s National Cancer Institute (NCI) to develop a cloud-based platform that will serve as a large-scale data repository and provide the...
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Genomics and Global Health - Pardis Sabeti, Charles Rotimi and Seema Kumar

September 30, 2014 - Genomics and Our Health: What does the future hold? A closing symposium for the exhibition - Genome: Unlocking Life's Code - that explores the potential of genomics to...
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Big genomic data on Google Cloud Platform

As the cost of DNA sequencing has dropped, the volume of data produced has risen into the petabytes. Google is working with the genomics community to define ...
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PSI 2014_International Proteomics Conference@IITB

We are pleased to announce that 6th annual meeting of PSI and International Proteomics Conference is scheduled at IIT Bombay, Mumbai from 6th - 11th Dec 2014...
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GTPB: HPND12 - Hunting for Promoters with NGS data

GTPB: HPND12 - Hunting for Promoters with NGS data | Bioinformatics Training | Scoop.it
Pedro Fernandes's insight:

Course description:

This course is set-up to review the basic principles of gene regulation and the corresponding bioinformatic problems. It will start with the computational prediction of promoters and distant enhancers and will deal with the analysis of the structure of such regions by identifying binding sites for transcription factors. The most intriguing parts of genomes, still not completely understood, are the gene regulatory regions – mostly promoters and enhancers. A complete annotation of a newly sequenced genome has to address the identification of these regions in addition to the classical task of finding genes in terms of coding regions. Regulatory regions define when, where and under what conditions genes become active and, thus, are part of the fundamental function of a gene. In this course, we will overview some of the experimental methods such as next generation sequencing (NGS) techniques for genome-wide epigenetic analysis such as ChIP-seq, which have revolutionized our ways for studying the gene regulatory mechanisms. The attendees will learn about several techniques of finding promoters and enhancers and the principles on which these methods are based on. In the "hands on" exercises, several analytical tools will be introduced and the results critically evaluated to assess their reliability.

Objectives:

The course will consist of lectures that lay out the conceptual framework as needed and and "hands on" exercises, which will provide the practical insight on the use of the methods, gradually, in order to produce skills that can be used with a relatively high degree of independence. Participants will learn how to set-up some of the programs, and use publicly available servers for more complex analytical jobs, in an informed fashion, so that they fully understand the output generated and how its quality can be assessed. Participants will also learn the novel principles of organization of gene regulatory regions, which will help them to interpret their results of genomic and transcriptomic studies.

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Balti and Bioinformatics “On Air” Wednesday September 10th 2014 - Oxford Nanopore sequencing talks


Via Mel Melendrez-Vallard
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How Physics and Thermodynamics Help Assess DNA Defects in Cancer

How Physics and Thermodynamics Help Assess DNA Defects in Cancer | Bioinformatics Training | Scoop.it
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‘Big data’ cancer research has revealed a new spectrum of genetic mutations across tumors that need understanding.
Existing methods for analyzing DNA defects in cancer are blind to how those mutations actually behave.
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Changing how we think

Changing how we think | Bioinformatics Training | Scoop.it
I spoke earlier this week at the University of Bristol and I had a very nice time.  I met my old friend Davide Pisani and also Jacob Vinther, a really awesome palaeontologist.  I gave my talk and afterwards there was some coffee and cakes.
Pedro Fernandes's insight:

It would be really nice if James could share the content of this talk.Slides? Video?

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GTPB: BPB14 Bioinformatics using Python for Biologists

GTPB: BPB14 Bioinformatics using Python for Biologists | Bioinformatics Training | Scoop.it

Python is an object-oriented programming language that is ideal for biological data analysis. The course will start from zero knowledge, and introduce you to all basic concepts of Python such as calculating, organizing data, reading and writing files, program logic and writing bigger programs. All examples and practical sessions will focus on solving biological problems.

In particular the sessions will cover:
- working with DNA and protein sequences
- data retrieval from files and their manipulation
- running applications, such as BLAST, locally and from a scrip
- finding motifs in sequence
- parsing common file formats (Uniprot, GenBank, PDB, BLAST) with Biopython
- ways to find and correct program errors

The course will be highly interactive and the students will continuously put theory into practice while learning. By the end of the course, the participants will have a good understanding of Python basics and will have acquired the skills to manage any type of bioinformatics database record and to run applications from scripts. Basic Unix/Linux skills will be provided at the beginning of the course.

Pedro Fernandes's insight:

An excellent way for a biologist to start programming from scratch!

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Léo Felippe Dias's curator insight, November 10, 3:43 PM

Ótimo curso para aqueles que almejam utilizar o Python para bioinformática.

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New Details on Thyroid Cancer May Lead to More Precise Therapies

New Details on Thyroid Cancer May Lead to More Precise Therapies | Bioinformatics Training | Scoop.it
3 Bullets:
Papillary thyroid cancer represents 80 percent of all thyroid cancer cases.
Integrative analysis resulted in the detection of significant molecular alterations not previously reported in the disease.
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Xconomy.com Features 100K Project

Xconomy.com Features 100K Project | Bioinformatics Training | Scoop.it
Xconomy featured an article about the 100K Wellness Project. The article provides an introduction and follows with a Q&A with Dr. Nathan Price, who is Associate Director of ISB.
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Genomics and Our Health (Framing Talk) - Eric Green

September 30, 2014 - Genomics and Our Health: What does the future hold? A closing symposium for the exhibition - Genome: Unlocking Life's Code - that explores the potential of genomics to...
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Tute Genomics Explainer

The genome revolution starts now.
Pedro Fernandes's insight:

The need arises even more sharply  for providing tools that also use other data in integrative ways, together with genomic data.

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New Tool Uses 3-D Protein-DNA Structures to Predict Locations of Genetic ‘On-Off’ Switches

New Tool Uses 3-D Protein-DNA Structures to Predict Locations of Genetic ‘On-Off’ Switches | Bioinformatics Training | Scoop.it
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Novel systems approach uses high-resolution structures of protein-DNA complexes to predict where transcription factors (genetic switches) bind and regulate the genome.
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Roma Agrawal on bridging the diversity gap in engineering and inspiring a future generation

Roma Agrawal on bridging the diversity gap in engineering and inspiring a future generation | Bioinformatics Training | Scoop.it
Roma Agrawal: “We have to make sure stereotypes don’t get in the way of future choices.” (Image courtesy of Nicola Evans, WSP)

Roma is an Associate Structural Engineer at WSP where she spent six years working on The Shard.
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Balti and Bioinformatics - Yannick Wurm - YouTube

Why computing for genomics sucks! Recorded at Balti and Bioinformatics, Birmingham, 27th May 2014 http://pathogenomics.bham.ac.uk/blog/2014/05/balti-and-bioi...

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