http://cosmos-fp7.eu

EMBO Practical Course on Metabolomics Bioinformatics for Life Scientists 2016

Reza — Thu, 12 Nov 2015 01:03:46 +0000

EMBO Practical Course on Metabolomics Bioinformatics for Life Scientists

February 14 — 19, 2016

European Bioinformatics Institute, CB10 1SD, United Kingdom

Link: https://www.ebi.ac.uk/training/events/2016/embo-practical-course-metabolomics-bioinformatics-life-scientists-2

Date: A Six-day course: starting Sunday, February 14 2016 to Friday, February 19, 2016

Who is this course aimed at: This course is aimed at PhD students, post-docs and researchers with at least two or three year’s experience in the field of metabolomics who are seeking to improve their skills in metabolomics data analysis.

Topics covered:

Metabolomics study design, workflows and sources of experimental error, difference between target and un-target approaches.
Metabolomics data processing tools: hands on open source R based programs, XCMS, MetFrag, MetFusion, Metab, rNMR/BATMAN for LC-MS and GC-MS data.
Metabolomics data analysis: Using R Bioconductor, understanding usage of univariate and multivariate data analysis, data fusion concepts and data clustering
Metabolomics downstream analyses: KEGG, BioCyc, MetExplore and Cytoscape for metabolic pathway and network analysis with visualisation of differential expression, understanding metabolomics flux analysis.
Metabolomics standards and databases: data dissemination and deposition in EMBL- EBI MetaboLights repository, review of collection and ever growing metabolomics online tools, resource and databases, COSMOS data standards, MSI (Metabolomics Standards Initiative)

We will have lively and interactive discussion throughout the course in addition to the hands-on data analysis and processing. We encourage you to bring problems you might have with a particular data set (YES, BRING YOUR DATA) and participate in group discussion. You might be asked to present your work and will participate in the discussions from day one.

For more details please have a look at the link below, or contact me Reza Salek.

https://www.ebi.ac.uk/training/events/2016/embo-practical-course-metabolomics-bioinformatics-life-scientists-2

Please make sure you have submitted a full application, as an incomplete application would not be eligible, deadline is 13 November 2015.

Open source software libraries for reading, and for some writing, mzML

Reza — Wed, 21 Oct 2015 18:27:02 +0000

An important aspect is that metabolomics studies might comprise many raw data files, so the conversion from the vendor formats should not involve expensive manual intervention to add information beyond what is already stored in the instrument software. Furthermore, command line converters are easier to incorporate into local data processing pipelines. For bioinformaticians developing either software or databases, it is highly recommended to use existing I/O parsing software and libraries. Several such mzML libraries have been developed for different programming languages and software frameworks, summarised in Table below.

Language	Library/API	URL	License
Java	jmzML	https://code.google.com/p/jmzml/	Apache license 2.0
Java	jmzreader	https://code.google.com/p/jmzreader/	Apache license 2.0
C++	OpenMS	http://open-ms.sourceforge.net/	BSD
C++	Proteowizard	http://proteowizard.sourceforge.net/	Apache license 2.0
Python	pymzML	http://pymzml.github.io/	LGPL v3
R	mzR	http://bioconductor.org/packages/mzR/ https://github.com/sneumann/mzR	Artistic-2.0
MatLab	MSiReader	http://www4.ncsu.edu/~dcmuddim/msireader.html	BSD 3-clause
Ruby	mspire	https://github.com/princelab/mspire	MIT
Perl	MzML::Parser (CPAN)	https://github.com/Leprevost/MzML-Parser http://search.cpan.org/dist/MzML-Parser/	Dual: GPL or artistic license

See also http://www.ms-utils.org/wiki/pmwiki.php/Main/SoftwareList for a growing link of MS related software

Tags:

metabolomics

standards

tools

Workshop on metabolomics data processing

Reza — Fri, 14 Aug 2015 15:21:15 +0000

Invitation to

Workshop on metabolomics data processing

September 2, 2015 Steno Diabetes Center, Gentofte, Denmark

Modern analytical technologies afford comprehensive and quantitative investigation of a multitude of different metabolites. Typical metabolomic experiments can therefore produce large amounts of data. Handling such complex datasets is an important step that has big impact on extent and quality at which the metabolite identification and quantification can be made, and thus on the ultimate biological interpretation of the results. Increasing interest in metabolomics thus led to resurgence of interest in related data processing. The aim of the workshop is to introduce and discuss (1) state-of-the-art tools for metabolomics data processing, (2) emerging standards related to data exchange and software development tools, and (3) the key challenges in this field. A hands-on workshop on the use of the popular open source package MZmine will also be given by the current developers of the software. This workshop is motivated by the visit of Tomaš Pluskal at Steno Diabetes Center during the month of September, prior to his move to Whitehead Institute for Biomedical Research in Cambridge, MA. During his visit at Steno, Tomaš will focus on the completion of the next major version of the MZmine software. The workshop is supported by EU project COSMOS (COordination of Standards in MetabOlomicS).

Program, September 2, 2015 Venue: NSK auditorium (Steno Diabetes Center, Niels Steensens Vej 6) 09:00 Arrival, coffee, introduction 09:30 Tomaš Pluskal (visiting scientist, Steno Diabetes Center) – The future of MZmine

processing: MZmine 3 and Mass Spectrometry Development Kit (MSDK) 10:10 Giorgio Tomasi (University of Copenhagen) – Pre-processing of GC-MS and (U)HPLC-MS

metabolomics data using XCMS and CAMERA 10:35 Coffee break 10:50 Søren Furbo (University of Copenhagen) – Pixel-based analysis of GC×GC-ToFMS data 11:15 Thomas Dyrlund (Steno Diabetes Center) – Automated quality control of large scale LC-

MS metabolomics data

11:40 Lunch (NSK aula)

12:30 Hands-on workshop – MZmine, led by Tomaš Pluskal and Thomas Dyrlund (NSK building,

ground floor)

15:30 Closing of the meeting

Registration Registration is free of charge. Please register by Friday, August 28, at the following web site: http://goo.gl/forms/04QTOfZNP9

Greetings from the organizing committee Matej Orešič (mtjo@steno.dk) Thomas Dyrlund (tfrd@steno.dk) Tuulia Hyötyläinen (tuhy@steno.dk) Pia Friis (pafs@steno.dk)

Metabolomics 101 - From Experimental Design and Sample Preparation to Data Quality, Data Standards and Data Sharing Overall goals

Reza — Sat, 06 Jun 2015 12:21:01 +0000

This Workshop is organized by COSMOS and the Data Standards Task Group of the Metabolomics Society presenting during the annual Metabolomics Society conference in San Francisco June 2015

Join is our workshop: http://metabolomics2015.org/index.php/program/oral-presentations-detail/...

In part 1, participants will learn the key concepts in establishing a metabolomics study, and how to design and complete a successful experiment. Part 2 will provide an overview of current practices, and educate new and experienced metabolomics researchers in the requirements for quality assurance and quality control. Part 3 will educate researchers in metabolomics data sharing, data standards, and data exchange Target audience: This is a ‘General Practices’ theme aimed at beginners starting in the metabolomics field, graduate students, post-doctoral researchers, principle investigators, and new investigators. Attendees will learn about experimental design, sample preparation, and metabolomics data sharing and standards.

Speaker Line-up:

Part 1: Charmion Cruickshank-Quinn (University of Colorado, Denver), Samantha Bokatzian (University of Colorado, Denver)

Part 2: Dan Bearden (NIST, USA), Warrick Dunn (Birmingham, UK)

Part 3: Reza Salek (EMBL-EBI, UK), Steffen Neumann (IPB Halle, Germany), Philippe Rocca-Serra (University of Oxford, UK)

BioMedBridges and COSMOS highlight emerging role of metabolomics

Reza — Mon, 23 Mar 2015 17:00:19 +0000

BioMedBridges and the COSMOS project have issued a joint statement on the need for data standardisation in metabolomics. The joint statement can be accessed via BioMedBridge website or COSMOS website.

Metabolomics is one of the latest -omics sciences and there is a growing interest for its application in prognosis, diagnosis, patient stratification and personalized medicine. For this reason, biomedical research infrastructures are strongly interested in the development of this technology. Because metabolomics is multidisciplinary in nature, it could rapidly become an “experimental bridge” between the different communities served by the research infrastructures.

To achieve this, a strong requirement is that any methodology deployed can be applied in the various biomedical contexts with little or no modification. The COSMOS project represents a successful ongoing effort, and BioMedBridges is instrumental in providing knowledge on how to harmonize data and metadata produced by users of the biomedical research infrastructures.

In a joint statement, the COSMOS and BioMedBridges projects have highlighted the emerging role of metabolomics in biomedical research and stress the need for further efforts in developing common standards and procedures to harmonize both experimental procedures and the data and metadata produced in metabolomics.

BioMedBridges and COSMOS: joint statement on the need for data standardisation in metabolomics

The 8th International Biocuration Conference (IBC) will be held in April 23-26, 2015, at Beijing Friendship Hotel, Beijing, China.

Reza — Sat, 14 Mar 2015 17:30:00 +0000

Omics studies, such as those of genomics, transcriptomics, proteomics, epigenomics and metabolomics, have accumulated a large volume of biomedical data. However, the promise to translate these big data into biomedical knowledge can be realized only if they are standardized to be interoperable, complete to ensure data integrity, and consistent in data content. Biocuration provides tools and procedures critical in realizing the promise. This conference is ogranized by International Biocuration Conference (IBC) runig by International Society of Biocuration. IBC is the global discussion platform for biocurators, bioinformaticians, data scientists, as well as any biomedical researchers and practitioners who care about data quality and interoperability, and interested in the exploration of a great application potential by data-driven knowledge discovery. (ISB, http://www.biocuration.org)

more infrmation can be found at: (http://biocuration2015.cbb.big.ac.cn). COSMOS will present "Standardization and global knowledge exchange in metabolomics by Reza Salek EMBL-EBI"

First Brazilian Workshop on Bioinformatics/Chemometrics for Metabolomics 13th - 14th March 2015

Reza — Sat, 14 Feb 2015 17:15:08 +0000

The First Brazilian Workshop on Bioinformatics/Chemometrics for Metabolomics aims to group expertise on metabolomics data analysis spread in different science fields in the Brazilian community. It is also an attempt to strength community collaboration, exchanging resources and knowledge through the community mapping. The event is open to all scientific community. COSMOS will present "Data sharing and standards in metabolomics: What we can learn from other “omics” by Reza Salek"

Find more infromation at: http://nppns.fcfrp.usp.br/

EXPERT CENTER FOR METABOLOMICS

Reza — Fri, 30 Jan 2015 17:35:40 +0000

Having identified the benefits of metabolomics approaches for sample quality evaluation, various COSMOS partners, as well as some other private and public stakeholders, have established a consortium of institutions involved in metabolomics activities as a follow-up of the implementation of a working group between the NMR metabolomics working group of COSMOS and BioMedBridges described in Deliverable 6.2 (see the COSMOS website).

The consortium, named EXCEMET (Expert Center for Metabolomics; http://www.excemet.org/) proposes itself as a reference infrastructure for biobanks. The synergy arising from coordinated actions between these scientific entities is foreseen as a method to push forward the metabolomics field and to provide a scientific support for the development of validated quality control measures based on molecular profiling within biobanks. EXCEMET proposes itself as a reference infrastructure for biobanks and has been described as a model of a BBMRI-ERIC Expert Center. EXCEMET has been established as a not-for-profit public-private-partnership based on a consortium agreement between participants from academia and industry. The involvement of the Medical University of Graz, with a research unit lead by Prof. Kurt Zatloukal, who coordinated the preparatory phase of the European biobanking and biomolecular research infrastructure (BBMRI) during the 7th EU framework programme, testifies the close links that have been established between the metabolomics and the biobanking community. Prof. Zatloukal is also member of the Advisory Board of COSMOS.

EXCEMET will complement the activities of the biobanks, extending the access from high quality samples to advanced biomolecular analyses and the dissemination of curated knowledge from those analyses in open-access, long-term maintained databases.

EXCEMET foresees to contribute assessing and developing a number of critical steps of the overall workflow implemented at biobanks, in particular:

to check the performances of adopted procedures for sample storage, as different conditions may influence the molecular profiles;
to evaluate the effect of preanalytical steps on the sample quality and stability via metabolic profiling, to propose standard operating procedures (SOPs) to be implemented for deposition in biobanks;
to make a comparative evaluation of the various sample stabilizers and to provide hints for the new stabilizers;
to check quality/integrity of biobank samples, in terms of intactness of the original metabolome (good warranty of the intactness of the overall biomolecular profile);
to define shelf-life in biobanks;
to evaluate the minimum samples number to be tested for statistical significance;
to generate a common set of reference samples to be shared among the different members of EXCEMET, and to be used as common internal standards to improve interoperability across the centers;
to achieve technical developments for decreasing the minimal sample volume, increasing sensitivity/reduction of experiment time; reducing the costs, and improving reproducibility of the results, in order to propose a better service to biobanks.

The strong links and interactions between EXCEMET and COSMOS are witnessed by the presence of three COSMOS partners as members of the EXCEMET consortium. However EXCEMET is an open consortium and it is possible to include new additional partners at any time, especially other COSMOS partners.

Biomarkers for Brain Disorders: Challenges and Opportunities 1-3 February 2015 Wellcome Trust Genome Campus, Cambridge, UK

Reza — Wed, 14 Jan 2015 07:45:33 +0000

The 3rd Wellcome Trust Scientific Conference on Biomarkers for Brain Disorders: Challenges and Opportunities was held at Wellcome Trust Genome Campus, Cambridge, UK. The discovery and validation of biomarkers across neuroscience is an important challenge for early diagnosis of disease and for the development of therapeutics. Methodological and regulatory aspects of biomarker identification and qualification across a wide spectrum of neurodegenerative diseases will be discussed. There will also be a series of break-out sessions for in-depth discussions on cognitive and functional biomarkers, identifying the ‘gaps’ in developing therapeutics, and the analytical and clinical standards required in ‘big data’ projects. COSMOS presented "Standardisation, big data and global knowledge exchange in metabolomics: an opportunity for brain biomarker researchby Reza Salek, EMBL-EBI, UK"

EMBO Practical Course on Metabolomics Bioinformatics for Life Scientists 2015

Reza — Fri, 21 Nov 2014 11:39:47 +0000

This is the 3rd edition of successful hands on data analysis course in metabolomics.

Venue: European Bioinformatics Institute, CB10 1SD, United Kingdom

See map: Google Maps

Date: Monday, February 16, 2015 - Friday, February 20, 2015

Who is this course aimed at: This course is aimed at PhD students, post-docs and researchers with at least two or three year’s experience in the field of metabolomics who are seeking to improve their skills in metabolomics data analysis.

Topics covered:

• Metabolomics study design, workflows and sources of experimental error, differences between target and un-target approaches.

• Metabolomics data processing tools: hands on open source R based programs, XCMS, MetFrag, MetFusion, rNMR, BATMAN and Chenomx.

• Metabolomics data analysis: Using R Bioconductor, understanding usage of univariate and multivariate data analysis, data fusion concepts and data clustering.

• Metabolomics downstream analyses: KEGG, BioCyc, MetExplore and Cytoscape for metabolic pathway and network analysis with visualisation of differential expression, understanding metabolomics flux analysis.

• Metabolomics standards and databases: data dissemination and deposition in EMBL- EBI MetaboLights repository, tutorials on collection and ever growing metabolomics online resource, COSMOS data standards, MSI, etc.

We will have lively and interactive discussion throughout the course in addition to the hands-on data analysis and processing. We encourage you to bring problems you might have with a particular data set or study for group discussion. You will be asked to present your work and participate in the discussions from day one.

For more details please have a look at the link below, or contact me Reza Salek.

http://www.ebi.ac.uk/training/course/metabolomics2015

Please make sure you have submitted a full application, as an incomplete application would not be eligible, deadline is 1 December 2014.