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Bioinformatics Training
Bioinformatics, blended with education and health sciences subjects
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GTPB: PHSMCP15 Promoter hunting and systems modelling of cellular pathways - Home

GTPB: PHSMCP15 Promoter hunting and systems modelling of cellular pathways - Home | Bioinformatics Training | Scoop.it
Overview

This course starts by reviewing basic principles of gene regulation and how information is encoded in the huge part of genome - it's so called "non-coding" part. Bioinformatics plays a huge role in exploring how gene regulation works. We will introduce mathematical modelling of cellular pathways and address the interplay between feedback and feed-forward loops of regulation. We will see how a range of modelling techniques can help us to:

- find master regulators
- understand disease mechanisms
- build models for use in precision medicine
- design novel systems for biotechnology

Starting from techniques for the computational prediction of promoters and distant enhancers, we will deal with the analysis of the structure of regulatory regions by identifying binding sites for transcription factors. 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 determine where, under which conditions and when genes become active. Thus, they are a fundamental part of the definition of the function of a gene. We will have a chance to introduce and acquire *hands-on* practice in next generation sequencing (NGS) techniques for genome-wide epigenetic analyses such as ChIP-seq.

Then we will approach the analysis and modelling of biological systems from several practical angles. Systems biology and modelling are approched here from the interaction and network-based perspectives. We will introduce several pathway databases, such as Reactome, KEGG, TRANSPATH, TRANSFAC, ConsensusPathDB and use these information resources to perform pathway analysis. Next, we will use modelling of biological systems to look at different mathematical modelling strategies, such as Boolean networks and ordinary differential equation systems (ODEs). We will describe computational tools, like Cytoscape and CellDesigner, for the set-up and development of model prototypes and show further tools, such as Copasi, BioUML and PyBioS that can be used for parameter-fitting and sensitivity analysis.

We will follow-on by looking at methods for reconstructing gene regulatory networks from gene expression data. The application of such methods can reveal key nodes in networks as potential biomarkers or drug targets. Dynamic systems modelling will be used to check the consistency of target and biomarker predictions. We will show real examples of application of these methods for identification of disease related biomarkers, drug discovery and personalized medicine.

Special attention will be given to the application of the above mentioned methods in designing novel biological systems, in the growing field of Synthetic Biology.

Methods

Participants 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. The course sessions will consist of lectures that lay out the conceptual framework as needed, 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 their 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.

The course will provide sufficient skills for the participants to address problems using open source software and freely accessible data resources. It will also be a chance to use commercially licensed resources such as TRANSFAC or the geneXplain integrated analytic platform for specific purposes.

Pedro Fernandes's insight:

Learn how to find promoters in NGS data an how to use genes and promoters to produce inferences at the pathway and system levels.

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The rise of the ‘Data Journal’

The rise of the ‘Data Journal’ | Bioinformatics Training | Scoop.it
The rise of the ‘Data Journal’
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Excellent source of information

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Electronic Health Records (EHR) Market Size, Share, Growth, Analysis And ... - MarketWatch

Electronic Health Records (EHR) Market Size, Share, Growth, Analysis And ... - MarketWatch | Bioinformatics Training | Scoop.it
Electronic Health Records (EHR) Market Size, Share, Growth, Analysis And ...
MarketWatch
Growing demand for digitalization and automation in healthcare is one of the major divers for the growth of electronic health records market.
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GTPB: IB15F Introductory Bioinformatics, First course - Home

GTPB: IB15F Introductory Bioinformatics, First course - Home | Bioinformatics Training | Scoop.it
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with David P Judge, Pedro L Fernandes and Javier Santoyo-Lopez

 

Overview

This is an entry level course aimed that those with a reasonable biological background but no significant experience with bioinformatics. The course is broadly based around a series of exercises in which a combination of simple analytical tools and reference to publicly available databases is applied to the investigation of a single human gene. The training manual for the course is comprised of detailed instructions for the tasks undertaken. Included are, questions (with answers) and discussion of and the interpretation of the results achieved.

Participants are asked to imagine an interest in the disease aniridia. Course exercises then provide extremely detailed instruction leading participants to discover the gene primarily associated with this disease and all that is interesting about that gene and its protein products.

This course will also provide a soft introduction to Next Generation Sequencing (NGS) data analysis. This part of the course aims at providing basic skills that are needed when one needs to process NGS data, such as evaluating data quality, trimming sequences, changing data formats, visualising data, etc. Then, participants will learn how to address a simple transcriptomics problem, stepwise, using open source bioinformatics tools.

 

Objectives

The operation of the various programs used in the exercises will be explained, but only to the extent that allows a user to select parameters intelligently and to interpret results.

The course will provide participants with an awareness of a wide range of bioinformatics tools and sufficient experience to use those tools in basic investigations with a relatively high degree of user independence.

In the training course design, this is intentionally built-in, to allow us to show a wide range of analytical techniques while providing enough experience to break the ice in all of them.

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Could Video Feedback Replace the Red Pen?

Could Video Feedback Replace the Red Pen? | Bioinformatics Training | Scoop.it
Stills from a video critique by Monash U.’s Michael Henderson.
Writing useful comments on students’ work can be a fine art.
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Rescooped by Pedro Fernandes from Bioinformatics Software: Sequence Analysis
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AtCAST3.0 Update – A web-based tool for analysis of transcriptome data by searching similarities in gene expression profiles | RNA-Seq Blog

AtCAST3.0 Update – A web-based tool for analysis of transcriptome data by searching similarities in gene expression profiles | RNA-Seq Blog | Bioinformatics Training | Scoop.it
In transcriptome experiments, the experimental conditions (e.g., mutants and/or treatments) cause transcriptional changes. Identifying experimental conditions

Via Mel Melendrez-Vallard
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Measuring intra-species diversity using high-throughput sequencing

Measuring intra-species diversity using high-throughput sequencing | Bioinformatics Training | Scoop.it
This practical course aims to show evolutionary biologists and population geneticists the potentials and perils of using high throughput sequencing to estimate intra-species genetic diversity. Participants will have the opportunity to interact with experienced researchers that have successfully applied the technology in a wide variety of high impact studies, and learn from their successes as well as from their failures. Participants will not only listen to theoretical lectures, but will also practice some of the techniques used in those high impact studies. Participants are strongly encouraged to bring their own projects for discussion and experiment novel techniques with their data.
Pedro Fernandes's insight:

Registration and abstract deadline:March 31st 2015 !

 

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Rescooped by Pedro Fernandes from Virology and Bioinformatics from Virology.ca
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Chimps And Gorillas Desperately Need Ebola Vaccine Too – Virus Has Wiped Out A Third Of Them | IFLScience

Chimps And Gorillas Desperately Need Ebola Vaccine Too – Virus Has Wiped Out A Third Of Them | IFLScience | Bioinformatics Training | Scoop.it
There is a side to the Ebola crisis that, perhaps understandably, has received little media attention: the threat it poses to our nearest cousins, the great apes of Africa.

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Rescooped by Pedro Fernandes from Virology and Bioinformatics from Virology.ca
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Cold coddles colds | Science News

Cold coddles colds | Science News | Bioinformatics Training | Scoop.it
Antiviral responses aren’t as effective against common cold viruses in cooler temperatures.

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Benchmarking variation and RNA-seq analyses on Amazon Web Services with Docker

Benchmarking variation and RNA-seq analyses on Amazon Web Services with Docker | Bioinformatics Training | Scoop.it
Overview We developed a freely available, easy to run implementation of bcbio-nextgen on Amazon Web Services (AWS) using Docker. bcbio is a community developed tool providing validated and scalable...
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Rescooped by Pedro Fernandes from Health and Biomedical Informatics
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Teaching Bioinformatics in Concert

Teaching Bioinformatics in Concert | Bioinformatics Training | Scoop.it
PLOS Collections: Article collections published by the Public Library of Science

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Welcome! — Practical bioinformatics needs survey 1.0 documentation


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bioinformatics - fastq-dump using mkfifo to stream data - Biology Stack Exchange

bioinformatics - fastq-dump using mkfifo to stream data - Biology Stack Exchange | Bioinformatics Training | Scoop.it
Biology SE: fastq-dump using mkfifo to stream data http://t.co/UfFVwpxLxH #bioinformatics

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GTPB - the Gulbenkian Training Programme in Bioinformatics

GTPB - the Gulbenkian Training Programme in Bioinformatics | Bioinformatics Training | Scoop.it

Bioinformatics hands-on training in short fece-to-face courses. GTPB provides skills in...

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Check the events on Facebook (also the past ones)

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GTPB: SMLMC15 - Structural Modelling for Large Macromolecular Complexes - Home

GTPB: SMLMC15 - Structural Modelling for Large Macromolecular Complexes - Home | Bioinformatics Training | Scoop.it
Pedro Fernandes's insight:
Overview

We will present a range of techniques to generate, analyse, and optimise models of proteins, RNA, and their complexes. We will talk about new approaches to structure determination of macromolecules and macromolecular complexes. During the practical sessions participants will learn how to use methods for modelling protein and RNA 3D structures such as Modeller and ModeRNA. Also we will focus on methods dedicated to protein-RNA complexes modelling, e.g. by combining data from low-resolution density maps, SAXS and biochemistry. In particular, we will present how to use PyRy3D, a computational tool to build models of macromolecular complexes based on data from various sources.
Participants will be able to bring-in specific biological questions and/or their on data to work with during the course.

Target Audience

The course has been designed for molecular and structural biologists, bioinformaticians and biotechnologists and other scientists interested in modelling of biological complexes. The content is suitable for researchers, both at the graduate and post-graduate levels.
Minimal levels of computer usage skills are required. We anticipate the participants to have a wide diversity of interests in biological complexes and their structures. It is likely that they may also aim at getting involved in generating structural models for complexes of interest, but that does not have to be the case for all the participants: they may, for example, just want to explore publicly available data.

Course Pre-requisites

Graduate level knowledge in Life Sciences, interest in structural biology.

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Rescooped by Pedro Fernandes from Bioinformatics Software: Sequence Analysis
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DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis

DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis | Bioinformatics Training | Scoop.it
My R/Bioconductor package, DOSE, published in Bioinformatics.



Summary: Disease ontology (DO) annotates human genes in the context of disease.

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Rescooped by Pedro Fernandes from Virology and Bioinformatics from Virology.ca
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A Third Rotary Motor Has Now Been Found in Bacteria

A Third Rotary Motor Has Now Been Found in Bacteria | Bioinformatics Training | Scoop.it
Evolution News and Views (ENV) provides original reporting and analysis about the debate over intelligent design and evolution.

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Ed Rybicki's curator insight, March 8, 4:21 PM

They go on a bit about "irreducible complexity", but if yoiu ignore that, it's really interesting: like finding your car has a crankshaft you didn't know about!

Rescooped by Pedro Fernandes from Virology and Bioinformatics from Virology.ca
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Bio Databases 2015

Bio Databases 2015 | Bioinformatics Training | Scoop.it
Something interesting happened in 2014. The total number of databases that Nucleic Acids Research (NAR) tracks dropped by three databases! What happened?  Did people quit making databases?  No.

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Pedro Fernandes's insight:

"This year, the “dead” databases (links no longer valid) outnumber the new ones."

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Rescooped by Pedro Fernandes from Bioinformatics Software: Sequence Analysis
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Benchmarking variation and RNA-seq analyses on Amazon Web Services with Docker

Benchmarking variation and RNA-seq analyses on Amazon Web Services with Docker | Bioinformatics Training | Scoop.it
Overview We developed a freely available, easy to run implementation of bcbio-nextgen on Amazon Web Services (AWS) using Docker. bcbio is a community developed tool providing validated and scalable...

Via Mel Melendrez-Vallard
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Rescooped by Pedro Fernandes from Natural Products Chemistry Breaking News
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Bioinformatics: The Next Frontier of Metabolomics - Analytical Chemistry (ACS Publications)

Bioinformatics: The Next Frontier of Metabolomics - Analytical Chemistry (ACS Publications) | Bioinformatics Training | Scoop.it
Anal Chem. 2015 Jan 6;87(1):147-56. doi: 10.1021/ac5040693. Epub 2014 Nov 20.Bioinformatics: the next frontier of metabolomics.Johnson CH1, Ivanisevic J, Benton HP, Siuzdak G. 

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Rescooped by Pedro Fernandes from Bioinformatics Software: Sequence Analysis
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Building Bioinformatics Solutions: with Perl, R and MySQL

Building Bioinformatics Solutions: with Perl, R and MySQL Offer Price $128.25 ISBN:0199230196 Authors Conrad Bessant, Ian Shadforth, Darren Oakley List Price : $135.00 Availablity Usually ships in 24 hours Publisher : Oxford University Press, USA...

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Rescooped by Pedro Fernandes from Virology and Bioinformatics from Virology.ca
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Vaccines Work. Here Are the Facts.

Vaccines Work. Here Are the Facts. - The Nib - Medium
The risks, the misinformation, and the science behind history’s greatest life saver

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Rescooped by Pedro Fernandes from Bioinformatics Software: Sequence Analysis
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Compression of High Throughput Sequencing Data with Probabilistic de Bruijn Graph « Homolog.us – Bioinformatics

Compression of High Throughput Sequencing Data with Probabilistic de Bruijn Graph « Homolog.us – Bioinformatics | Bioinformatics Training | Scoop.it
@RayanChikhi mentioned in twitter about this new paper –
“A super-efficient de novo read compression algorithm (Leon) from @GuillaumeRizk et al.

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Rescooped by Pedro Fernandes from Bioinformatics Software: Sequence Analysis
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The Sorghum Transcriptome Database | RNA-Seq Blog

The Sorghum Transcriptome Database | RNA-Seq Blog | Bioinformatics Training | Scoop.it
In transcriptome analysis, accurate annotation of each transcriptional unit and its expression profile is essential. A full-length cDNA (FL-cDNA) collection

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Rescooped by Pedro Fernandes from Bioinformatics Software: Sequence Analysis
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Identifying and correcting errors in draft genomes

Identifying and correcting errors in draft genomes | Bioinformatics Training | Scoop.it
Over the past decade we have seen an exponential increase in the number of sequenced, assembled, and annotated genomes. These these genomes are essential for pretty much any genomics research. If y...

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