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The core research objectives of Mr. SymBioMath are:

Research on the Big-Data problems and computational intensive applications in high-performance computing:

New software libraries for out-of-core management of Big-Data, specially for I/O
Reduction of the computational space and runtime for all-all sequences
New data structures for in-core data management to reduce memory demand

New data processing applications in comparative genomics, especially those related to Big-Data sets, to allow genome-wide association studies, such as:

Modelling evolutionary events (SNP, mutations, translocations, deletions, duplications, inversions, etc.) aimed to understand evolution and extrapolate from them the divergence between sequences for phylogenetic tree construction
Comparison and synthesis of inter-genome distances
Gene-Gene interactions studies correlated with phenotype data

Implementing and packing commercial application prototypes to evaluate the potential for their exploitation in biomedical cases, in concrete in the study of

Adverse reactions to treatment in allergic patients
Interfacing, visualisation, and integration of external data sources as well as functional annotations

Agenda:

Tuesday, 10^th of September: Bioinformatics

Time	Presenter	Content
8:30 - 9:00		Registration
9:00 - 9:15	Oswaldo Trelles (UMA, Spain)	Welcome to the summer school
9:15 - 11:15	Alois Regl (JKU Linz, Austria)	- Introduction to bioinformatics - Sequence analysis basics
	Coffee break
11:45 - 13:30	Oswaldo Trelles (UMA, Spain)	Comparative genomics scenarios in Mr. SymBioMath
	Lunch
14:30 - 16:30	Jose Ramon Valverde (Centro National de Biotechnologia, Spain)	Metagenome analysis

Wednesday, 11^th of September: Biomedicine and Systems Biology

Time	Presenter	Content
8:45 - 9:00	James Perkins (SAS, Spain)	Introduction and overview of the day's presentations
9:00 - 9:45	Miguel Blanca, M.D. (Hospital Carlos Haya, Malaga)	Introduction to allergies
9:45 - 10:30	Jose Antonio Cornejo (Hospital Carlos Haya, Malaga)	Using high-troughput studies (e.g. GWAS) to find genes involved in disease and patology
10:30 - 11:15	Ulrich Bodenhofer (JKU Linz, Austria) (TBC)	Overview of GWAS Data analysis
	Coffee break
11:30 - 12:30	Miguel Angel Medina (Biochemistry Dep., UMA, Spain)	An overview of systems biology
12:30 - 13:00	Juan Antonio Ranea (UMA, Spain)	Graphical models of networks and their analysis
	Lunch
14:00 - 14:35	Armando Reyes Palomares (Biochemistry Dep., UMA, Spain)	Tools to investigate the genetic basis of disease
14:35 - 15:10	Aurelio Moya (Biochemistry Dep., UMA, Spain)	Systems pharmacology - using biological networks for drug repositioning
15:10 - 16:30	Patrick Aloy (Institute for Research and Biomedicine, Barcelona, Spain)	Systems biology: Combining wet lab and dry lab experiments
16:30 - 16:50	Marc Streit (ICG, Johannes Kepler University Linz, Austria)	Visualizing bio-molecular data

Thursday, 12^th of September: Cloud computing

Time	Presenter	Content
8:45 - 9:00	Michael Krieger (RISC Software, Austria)	Introduction and overview of the day's presentations
9:00 - 10:00	Paul Heinzlreiter (RISC Software, Austria)	Overview on Cloud Computing
10:00 - 11:00	Michael Krieger (RISC Software, Austria)	Hadoop, HBase, And MapReduce (Theory)
	Coffee break
11:30 - 13:00	Paul Heinzlreiter (RISC Software, Austria)	Cloud Computing (Practice)
	Lunch
14:00 - 16:30	Michael Krieger (RISC Software, Austria)	Hadoop, HBase, and MapReduce practice

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Overview

This course will provide an overview of key issues that affect metabolomics studies,bioinformatics tools, and procedures for the analysis of metabolomics data. It will be delivered using a mixture of lectures, computer-based practical sessions and interactive discussions. The course will provide a platform for discussion of the key questions and challenges in the field of metabolomics.

Audience

This course is aimed at PhD students and researchers with a minimum of one year’ s experience in the field of metabolomics who are seeking to improve their skills in metabolomics data analysis. Participants must have experience using R (including a basic understanding of the syntax and ability to manipulate objects) and the UNIX/LINUX operating system.

Syllabus, Tools and Resources

During this course you will learn about…

Metabolomics study design, workflow and sources of experimental error
Metabolomics data processing: R, XCMS, MetFrag, NMR tools, …
Metabolomics data analysis: R, Bioconductor, data fusion, univariate and multivariate data analysis, data clustering and correlation methods…
Metabolomics downstream analyses: MetExplore, Cytoscape plugin, metabolic pathway analysis, visualisation, differential expression, metabolomics flux.
Metabolomics standards and databases: data dissemination and deposition in EBI-MetaboLights, ISATools and COSMOS

Learning Objectives

After this course you should be able to…

Discuss major principles of metabolomics experimental design and factors that impact upon subsequent analysis
Identify strengths and weaknesses in a variety of metabolomics analytical approaches
Use a range of Bioinformatics software to pre-process, process and analyse metabolomics data
Discuss current trends and challenges in metabolomics

Application registration closes 17 January 2014 (12:00 midday GMT). There will be a maximum of 25 participants on this course. Successful applicants will be notified by 31 January 2014 and will then be asked to confirm their place on the course by re-registering and paying the course fee.

Contact:
Reza Salek , EMBL-EBI & Cambridge University, UK

Science Club for Girls (SCFG) is looking for some inspiring mentors to guide eager young women through our STEM Internship Program. Our goal is to expand the program, piloted last year with support from the Massachusetts Life Science Center. You can make this a reality.

If you want to energize your lab or company, have projects that are accessible, and are excited about diversifying the STEM landscape, please read on!

The STEM Internship Program is an opportunity for young women, primarily from traditionally underrepresented economic and racial groups, to gain authentic, hands-on experience with science, technology, engineering, and mathematics (STEM), and increase their confidence and sense of self.

Started in 2012, the program broadens participation by matching 16- to 18-year-old young women with mentors in academic and industry settings to complete capstone projects. In our first year, we placed six students in internships at Boston University, Harvard University, and Aurora Flight Sciences, where they completed projects ranging from genetics to behavioral biology toengineering. At the end of their internships, 100 percent of participants reported that their relationships with their mentors and participation in the program helped them develop strong lab skills, more confidence in a lab setting and in their science abilities.

We ask internship mentors to make the following commitments:

> Devote 5-6 hours per week from October to May. This includes 3 hours of supervision when the intern is on site, and ~2 hours of prep.
> Provide background reading material.
> Complete a 45-minute online training to better understand SCFG and our philosophy.
> Attend a 2-hour Mentor Training in September so you know how to work with teens.
> Attend an optional event during the year to cheer your intern on.
> Hold monthly 15-20 minute phone check-ins and agree to site visits by our Internship Program Manager once a semester, so we can troubleshoot and adjust if necessary.
> Attend the year-end showcase event in May to celebrate.

SCFG provides STEM interns with support and training at bi-monthly workshops that cover essential college readiness, career building, and professional skills. With guidance from SCFG and internship mentors, STEM interns will complete capstone projects, which they present at the Cambridge Science Festival Science Carnival and SCFG’s annual teen showcase, CELLSebration, in May.

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Source:hattiesburgamerican

Bioinformatics will be the topic of the next Science Café at 6 p.m. Monday in the Cook Library Art Gallery (next to Starbucks in Cook 105A).

A Science Café’s casual meeting place, plain language, and inclusive conversation create a welcoming and comfortable atmosphere for people whose primary background may not be science.

Each meeting is organized around a scientific topic, with a presenter (usually a scientist) giving a brief overview and showing a short video to kick off the discussion.

Advances in molecular biology and genomic technologies have led to a massive amount of biological information generated by the scientific community. This abundance of genomic information has created an equal need for computerized databases to acquire, store, organize, archive the information – not to mention specialized tools to view and analyze the data. Thus, bioinformatics is born.

Join Dr. Mohamed O. Elasri, Professor in the Department of Biological Sciences, as we explore this relatively new field and what it could mean to you. Dr. Elasri is the Program Coordinator of the Mississippi IDeA Network of Biomedical Research Excellence. The group has established a core to fulfill the bioinformatics need of Mississippi scientists and to adequately prepare students to enter the various fields of research. Find out more about Mississippi IDeA Network of Biomedical Research Excellence at http://www.msinbre.net/ .

Science Cafés are free and open to the public. For more information, contact Tracy Englert at (601) 266-6396 or Tracy.Englert@usm.edu. Find out more about Science Cafés at http://sciencecafes.org/ .

Bioinformatics with Systems Biology (MSc)

Programme status: Fully Approved

Bioinformatics is a discipline that has arisen from the need to extract biologically useful information from the vast quantities of raw experimental data presently being generated in the biosciences.

This postgraduate degree is designed for students from a range of scientific backgrounds, who are particularly interested in the study of computational and scientific developments in bioinformatics, and the application of this knowledge to the fields of molecular and biological science.

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List of Candidates Shortlisted for Interview

1. Delhi (Including Kolkata)

2. Chennai (Including Bangalore, Hyderabad, Mumbai)

The dates for our 2013 Bioinformatics Short Course have been announced! We are having the 2013 Bioinformatics Short Course on September 16-20, 2013 right here at the University of California, Davis in Davis, CA. This intense week-long course provides the essential background for understanding the basics of sequencing technology, exploration into next-generation sequencing, de novo sequence assembly, and SNP discovery with or without a reference genome. We will also be looking at the technology and techniques behind RNA-seq, gene expression analysis, metagenomics and functional analysis using genome browsers, as well as high performance computing techniques for dealing with big data.

That’s just the mornings! Each afternoon is comprised of intensive hands-on training to enhance understanding of algorithms and the limitations of different sequencing technologies with focus on next-generation sequencing techniques and tools. Each day will feature challenges and focus on industry-standard tools such as Galaxy,data analysis in R, Cufflinks / TopHat for transcript assembly with a genome, Velvet genome assembler, Scythe / Sickle read trimmers, qrqc / FastQC read quality control tools, and more. Access to instructors is unrestricted in this collaboration-focused learning environment and personal attention is key.

If you would like to be notified via email on additional information, including when registration opens, please send us an email. Otherwise check back with us as we get closer to the date for more information.

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