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Bioinformatics Training
Bioinformatics, blended with education and health sciences subjects
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GTPB: HPND12 - Hunting for Promoters with NGS data

GTPB: HPND12 - Hunting for Promoters with NGS data | Bioinformatics Training | Scoop.it
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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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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.
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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 “On Air” Wednesday September 10th 2014 - Oxford Nanopore sequencing talks


Via Mel Melendrez-Vallard
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GTPB: TA-AFADM1 Transcriptome Assembly, Automatic Annotation and Data Mining

GTPB: TA-AFADM1 Transcriptome Assembly, Automatic Annotation and Data Mining | Bioinformatics Training | Scoop.it

This is a combined course in RNA-seq and functional annotation aimed at scientists working in next generation sequencing transcriptomics who want to extract the best possible information from their data. The course covers all aspects of RNA-seq analysis, from quality control, to mapping, reconstruction of transcripts and differential expression. Participants will learn how to deal with RNA-seq data both in the presence and absence of a reference genome.

The second part of the course is a practical workshop on Blast2GO, the most popular framework for functional annotation of sequence data. Participants will learn how to generate de novo functional labels, such as GO terms and KEGG pathways, for their sequence data and how to extract relevant information from these annotations, i.e. visualisation and enrichment analysis using the Gene Ontology. This part will be based on the use of the Blast2GO application and will mainly comprise exercises and practical cases. Participants may bring their own data.

 

With Stefan Goetz and Riccardo Alese Cigliano

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This  is a new edition of a combined RNAseq and Automatic Functional Annotation hands-on training course, successfully held here several times.

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How Streaming Media Threaten the Mission of Libraries

How Streaming Media Threaten the Mission of Libraries | Bioinformatics Training | Scoop.it
Digital music has made it easier to buy and share recordings. But try telling that to librarians.
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New Structural Map Helps To Understand Aggressive Tumors

New Structural Map Helps To Understand Aggressive Tumors | Bioinformatics Training | Scoop.it
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Aggressive tumor growth is linked to high activity of a macromolecular assembly called RNA polymerase I.
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Why Students Should Own Their Educational Data

Why Students Should Own Their Educational Data | Bioinformatics Training | Scoop.it
Designing a textbook or lecture with the average student in mind may sound logical. But L.
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Pimp your brain: Bioinformatics

Jan Lisec from the Max Planck Institute of Molecular Plant Physiology explains, in this "pimp your brain" episode, what bioinformatics is and why bioinformat...
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James Hane's curator insight, August 26, 2:41 AM

youtube captions make for an interesting read

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BIOCELLION: New Supercomputer Software Framework Models Biological Systems at Unprecedented Scales

BIOCELLION: New Supercomputer Software Framework Models Biological Systems at Unprecedented Scales | Bioinformatics Training | Scoop.it
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Computer simulation is a promising way to model multicellular biological systems to help understand complexity underlying health and disease.
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Can You Really Teach a MOOC in a Refugee Camp?

Can You Really Teach a MOOC in a Refugee Camp? | Bioinformatics Training | Scoop.it
Two men living in Dadaab, a refugee camp in Kenya, would watch lecture videos and take online quizzes at a nearby United Nations compound.
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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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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...

Via Docker
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Application Note about the GOBLET Portal (open access)

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A global repository of bioinformatics training materials.

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Analyzing Family Genomics Reveals New Culprit in Rare Disease

Analyzing Family Genomics Reveals New Culprit in Rare Disease | Bioinformatics Training | Scoop.it
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Adams-Oliver syndrome (AOS) is a rare congenital disease characterized by scalp lesions and limb defects. Additional vascular abnormalities and heart defects can lead to early death in some patients.
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That’s Not #Funny: Higher Ed’s Least Clever Twitter Accounts

That’s Not #Funny: Higher Ed’s Least Clever Twitter Accounts | Bioinformatics Training | Scoop.it
Earlier this month, a puckish Twitter user going by the handle @ProfJeffJarvis managed to provoke two actual professors into fits of outrage.
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Collaborative That Once Criticized Software Companies Becomes One

Collaborative That Once Criticized Software Companies Becomes One | Bioinformatics Training | Scoop.it
Ten years ago, a group of universities started a collaborative software project touted as an alternative to commercial software companies, which were criticized as too costly.
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As many academics as possible should be running Kuali's test drives: students, teachers, trainers, administrative staff members, librarians,etc.

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Evolution in the Anthropocene: Population Genomics of NYC Wildlife

This presentation describes ongoing efforts to develop white-footed mice (and a few other species) in New York City as models for examining the evolutionary implications of urbanization. Also...
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Tracking Cells from Well to Diseased

Tracking Cells from Well to Diseased | Bioinformatics Training | Scoop.it
KUOW's Marcie Sillman and producer Amina Al-Sadi interviewed Dr. Lee Hood about P4 medicine and the 100K Wellness Project. This 29-minute recording is a great conversation about Lee's vision for how to turn healthcare on its head.
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New $10.9 Million Grant from NIH

New $10.9 Million Grant from NIH | Bioinformatics Training | Scoop.it
The NIH's National Institute of General Medical Scienes has issued a Biotechnology Resource Grant of $10.9 million over five years to the National Center for Dynamic Interactome Research (ncdir.org) project.
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