How to obtain further information

The contact page of the EMBRACE website lists the names of the people whom you can contact for all kinds of information about EMBRACE. You can of course also contact the EMBRACE partner living nearest to you. If you are more interested in bioinformatics itself than in the technology that enables bioinformatics, you might also want to look at the BioSapiens WWW pages.

News

The main objective of the EMBRACE project, as the abbreviation already suggests, is to embrace the European science community. One of the vehicles to achieve this goal is by a large series of dissemination activities. The announcements for these activities as well as other news are listed in the archive below.

EMBRACE Project ends
Posted on Monday, 13th December 2010

The EMBRACE project has reached the end of its five-and-a-half year running period. Data has been integrated, webservices have been opened, people have worked together and all reports have been written. Bioinformatics in Europe has definitely benefited from the collaborative efforts and is stronger today as a result. The Embrace organisers would like to thank everyone who has contributed in the past five years to make the European Model for Bioinformatics Research and Community Education a huge success. Thank you!

 

EMBRACE Workshop: Next Generation Sequencing II
Posted on Thursday, 29th April 2010

Where: Bari, Italy

When: 16-17 June 2010

This workshop is a continuation of the previous workshop in Rome 2009. It is aimed at bioinformaticians interested in discussing issues related to the management of platforms and analysis of next-generation sequencing data. The workshop will include lectures by experts from relevant fields and corresponding practical sessions. Topics covered will include storage facilities for sequencing raw data, tools for genome mapping of sequence reads, sequence reads assembly, contig and scaffold generation, gene calling of mapped reads for digital analysis of gene expression, identification of structural genome variants by using long paired-end sequencing and tools for genome annotation.

The workshop will start June 16th at h 09:00 with a list of presentations on the topics such as de novo sequencing: analysis strategies, reference supported sequence assembly, re-sequencing: mapping and detection of variability, RNA-seq and digital gene-expression profiling, ChIP -seq, epigenetics, metagenomics, small RNA sequencing and genome annotation.

The second day will be dedicated to an extensive hack-a-thon session with real data analysis of some of the above mentioned topic. A poster session will be held in parallel.

After the work a sight-seeing tour will be offered to all the participants.

For more information, preliminary programme and registration (limited space of 30 participants) see:
http://www.nextgenerationsequencing.org/

 

EMBRACE Workshop for Web Service Providers: Syntax, Semantics and Publishing
Posted on Thursday, 7th April 2010

Topics: EMBRACE guidelines for design, semantic annotation and publishing of
SOAP-based Web Services in the area of Life Sciences.
Participants should already be familiar with web service concepts, and will preferably have prior experience with or involment in producing a Web Service.

Where: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark (near Copenhagen)

When: June 2-4, 2010

How: Hands-on exercises performed on the participants' own Web Services.

More info and registration (extended deadline: May 3rd): http://www.cbs.dtu.dk/courses/embrace/2010-06-02/

Final AGM registration open
Posted on Friday, 29th January 2010

The EMBRACE Final Annual General Meeting will be held in Amsterdam 20-21 May 2010.
For more information and to register, please click here.
The registration deadline is 16 April 2010.

Biocreative Workshop II.5, CNIO, Madrid, October 7th-9th 2009
Posted on Monday, 28th September 2009

The EMBRACE-ENFIN workshop on BioCreative II.5 will be held in Madrid at the CNIO from October 7th to 9th, 2009.
It will focus on the tasks created for the challenge, especially the extraction of protein-protein interactions (PPIs), with the background of creating structured annotations for full-text papers. These PPIs were generated by the paper authors themselves and MINT database curators (a PPI DB).
There will be invited speakers discussing various topics relevant to Information Extraction in Text Mining and the topic of digital annotations, meta-services and applications in Bioinformatics.
When interested, please register!

EMBRACE Workshop on Perl, SQL and Web Services, CBS, November 16-20, 2009
Posted on Wednesday, 26th August 2009

The workshop will be held at the Center for Biological Sequence Analysis (CBS), Technical University of Denmark. For registration and more information please see the workshop page (Registration deadline: September 30, 2009)

Description
The workshop is intended to give the participant an introduction to a set of skills needed to perform basic bioinformatics work without the assistance of professional programmers. It will cover a general-purpose scripting language (Perl), database manipulation (SQL) and programmatic access to remote resources (Web Services). Brief introductory lectures will be followed by extensive hands-on exercises aiming at the ability to develop clean, efficient Perl scripts accessing relational databases and remote resources. There will be template scripts to take home and develop further in the context of the participant's own work.

Embrace-Enfin workshop: Expression, interactions, and system level modeling
Posted on Tuesday, 16th June 2009

The EMBRACE grid and ENFIN (Experimental Network for Functional Integration) are organizing a joint workshop on expression, interactions and system level modelling

Please see the relevant website

Scope
Combining gene expression data with protein-protein and protein-DNA interactions data using computational methods has the potential to elucidate the regulatory mechanisms of biological processes. This workshop aims to bring together both experimentalists and computer scientists to discuss the latest advances in the field, including the tools and databases available for research community.

5th AGM finished, documents online
Posted on Thursday, 21st May 2009

The fifth EMBRACE AGM has been concluded.
The presentations can be found in the restricted area after logging in

5th AGM registration opened
Posted on Thursday, 05th March 2009

Registration for the 5th EMBRACE AGM is NOW OPEN. Please all register!
The registration deadline is 22 April 2009.

Contrary to earlier reports, the meeting will take place in Geneva, not in Lausanne.

The program and other information can be found online as well.

EMBRACE web services registry
Posted on Friday, 09th January 2009

EMBRACE now provides provides a Life Sciences Web Service registry via the EMBRACE Registry, in expectation of the unifying BioCatalogue

EMBL Heidelberg, Germany, 03 - 05 December 2008
Posted on Saturday, 13th September 2008

Exploring Modular Protein Architecture

EMBL Heidelberg, Germany, 03 - 05 December 2008

http://www-db.embl.de/jss/EmblGroupsOrg/conf_110

CBS/BioSys Workshop on R and BioConductor for Genomic Data Analysis
Posted on Friday, 05th September 2008

CBS/BioSys Workshop on R and BioConductor for Genomic Data Analysis

October 7-10, 2008 (optional introduction to R October 6-7)
Center for Biological Sequence Analysis
Department of Systems Biology
Technical University of Denmark

The focus will be the use of BioConductor for working with microarrays - Gene Expression as well as Genomic Variation. Examples during the workshop will include SNP and CNV microarray chips. Data visualisation in R will also be covered in the workshop. Course language is English.

The workshop assumes some programming experience, and basic familiarity with microarrays, statistics and their biological contexts. An optional introduction to R precedes the course and is open to all workshop participants.

More information, including application form available here

Deadline for applying: Sep 12, 2008. The applicants will be notified
by email of the status of their applications not later than Monday,
September 22, 2008.

Web Services in Systems Biology in Gothenburg, August 28th
Posted on Tuesday, 24th June 2008

Web Services in Systems Biology
Satellite workshop at the 9th International Conference in Systems Biology (ICSB) in Gothenburg, August 28th
http://www.embracegrid.info/page.php?page=training_report&tr=27

Further information:
http://www.molgen.mpg.de/~ICSB2008Workshop/index.html

Organiser
Ralf Herwig (Max Planck Institute for Molecular Genetics, Berlin, Germany, herwig@molgen.mpg.de) on behalf of the EU Network of Excellence EMBRACE.

2008 September 15-17, 8th workshop on Algorithms in Bioinformatics (WABI 2008)
Posted on Wednesday, 26th March 2008

The 8th workshop on Algorithms in Bioinformatics (WABI2008) will be held
in Karlsruhe, September 15-17, 2008.

Further info can be found at http://algo2008.org/doku.php/wabi

2008 May 18-20 Advanced Protein Domain Analysis
Posted on Friday, 07th March 2008

Advanced Protein Domain Analysis
Training Workshop
Lyon, May 18-20, 2008

Go to workshop page

4th EMBRACE Annual General Meeting
Posted on Monday, 03rd March 2008

The 4th EMBRACE Annual General Meeting will take place at Hotel Molkenkur, Heidelberg, on 22nd - 23rd April, 2008.

Please click here for registration and agenda.

August 28th, 2008 Web services
Posted on Monday, 11th February 2008

Web services in Systems Biology Workshop within the 9th International Conference on Systems Biology

August 28th, 2008, 9:00 AM - 18:00 PM

Organiser Ralf Herwig (Max Planck Institute for Molecular Genetics, Berlin, Germany, herwig@molgen.mpg.de )

Link for further information

Important: Deadline is March 1st 2008

2008 February 14th, EGEE User Forum meeting
Posted on Wednesday, 19th December 2007

The Embrace workshop held in conjunction with the EGEE User Forum in Clermont-Ferrand on Feb 14th 2008 in the afternoon.
The workshop will be the opportunity to review the progress accomplished in the development of web services interfaces to the bioinformatics data bases and tools. It will also be used to evaluate the evolution of the grid technology in the last 2 years in the perspective of a new technology recommandation to be produced by Embrace Work Package 3.
Registration will soon be available through the EGEE User Forum web page.

2008 Feb 6-8 Workshop on Client Side Scripting for Web Services
Posted on Friday, 07th December 2007

EMBRACE Workshop on Client Side Scripting for Web Services

http://www.cbs.dtu.dk/courses/embrace/2008-02-06/

February 6-8, 2008
Center for Biological Sequence Analysis
BioCentrum-DTU
Technical University of Denmark

2007 December 4-11 Webservices workshop in Manchester
Posted on Friday, 09th November 2007

Web Services are becoming an increasingly popular means of making bioinformatics tools availble to researchers via the internet, but deploying resources so as to make them robust and easy-to-use is not always straightforward. This workshop aims to give participants insight into the issues involved in exposing tools and databases as globally available resources using Web Service technology. The programme covers issues from the various low level technologies available, to the grand-challenges of Semantic Integration

Further information
Registration here

Lipari International Summer School on BioInformatics and Computational Biology
Posted on Tuesday, 16th October 2007

The Lipari International Summer School on BioInformatics and Computational Biology will be held on Lipari Island, Italy, June 14 - June 21, 2008

For more information see here - http://lipari.cs.unict.it/LipariSchool/Bio/index.php

November 7th - 9th, 2007 Applied Gene Ontology
Posted on Saturday, 06th October 2007

EMBRACE Workshop

"Applied Gene Ontology"

Bari, Italy
November 7th - 9th, 2007

More information

membrane protein bioinformatics - August 22nd - 23rd 2007
Posted on Tuesday, 07th August 2007

The EMBRACE workshop on membrane protein bioinformatics will take place
in Stockholm on August 22nd - 23rd 2007.
Look here for more information.

ECCB/ISMB meeting in Vienna in July 2007
Posted on Tuesday, 26th June 2007

EMBRACE will have a heavy presence at the ISMB/ECCB meeting in Vienna,
July 18-25. We will be highly present, present a poster, hand-out flyers
with information, and be available for people who want to discuss the
Grid and web-services.

Feel free to contact us while we are there; we are looking forward to that.

You can view the Embrace Web Services presentation from this meeting.

Deployment of Web Services for Biological Sequence Annotation May 31st - June 1s
Posted on Wednesday, 07th March 2007

We are pleased to announce that the registration for our workshop

"Deployment of Web Services for Biological Sequence Annotation"
May 31st - June 1st, 2007
Centre M??dical Universitaire (CMU), Geneva, Switzerland.

is now officially open at this URL:
http://www.ch.embnet.org/EMBRACE/Registration.php

Please note that the number of participants will be limited to 30.
The participation in the workshop is free of charge.

Modern computer tools for the biosciences, 22-23 March 2007
Posted on Thursday, 22nd February 2007

This workshop will focus on needs biologists have in relation to new tools and databases and the partners
will present new solutions created by the EMBRACE project.

More information and registration: http://teacher.bmc.uu.se/Moderntools/

The EMBRACE course on Workflows over Grid-based Web services...
Posted on Friday, 05th January 2007

The EMBRACE course on "Workflows over Grid-based Web services : General framework and a practical case in structural biology" will take place in Madrid on Monday 19th to Friday 23rd February 2007.

Click here for more information.

Web Services Workshop (Bergen, Norway, 4 - 13 December)
Posted on Wednesday, 11th October 2006

The Computational Biology Unit (CBU) and University of Manchester (UMAN) invite all EMBRACE partners to attend a Web services workshop in Bergen, Norway on 4-13 December. The goal of this workshop is to facilitate the completion of the Web service deliverables of month 24 for all EMBRACE partners.
Partners are free to choose the length of their stay any time during the 10 day workshop period, and individual assistance will be provided.

For more information and registration: www.cbu.uib.no/courses/embrace_workshop

EMBRACE RSMD Workshop, Uppsala 9-10 November 2006
Posted on Wednesday, 11th October 2006

This workshop will focus on Regulatory Sequence Motif Discovery tools and databases and web-services/grid aspects related to the EMBRACE project.

For more information see - http://teacher.bmc.uu.se/RSMD2006/

Workshop on Regulatory Sequence Motif Discovery (10th Nov 2006)
Posted on Wednesday, 04th October 2006

Workshop on Regulatory Sequence Motif Discovery, 10th November 2006. The Linnaeus Centre for Bioinformatics, SLU-UU, Sweden.

Contact: Erik.Bongcam@lcb.uu.se, David.Ardell@lcb.uu.se

The workshop format will be rather informal, and discussion will be encouraged. A list of confirmed speakers will be available soon.

EMBRACE - EGEE Tutorial (Clermont-Ferrand, October 9 - 13)
Posted on Friday, 04th August 2006

This tutorial aims to train system administrators in order to give them skills to install, configure and manage a complete Grid node using gLite 3.x. Preference is given to systems administrators within EMBRACE but the workshop is also open to other projects if space is available.

For more information please see http://agenda.cern.ch/fullAgenda.php?ida=a063215

Grid and Web Services technology for bioinformaticians (Helsinki, June 15-17)
Posted on Monday, 08th May 2006

Grid and Web Services technology have been increasingly approaching each other, thereby emphasizing the importance of interoperability, standards, and best practise.

The workshop aims to help the participants navigate the fast developing field of Web Services technology by giving practical information on using and creating Web Services. Some sessions are open to the public.

For more information visit here - http://www.csc.fi/english/research/sciences/bioscience/Courses_and_event...

Mutual Embrace WP3/EGEE/INFN Workshop
Posted on Monday, 08th May 2006

The Workshop on Grid data replication, consistency and requirements will be held in the INFN Pisa section, the 26th of May 2006.

It will focus on Grid data managements issues particularly as regards data replication and replica consistency requirements. Data replication is a main concern in the Grid community and replica consistency is the hardest topic of a replicated environment when replicas need to be updatable. Replicated data can be flat files and databases as well, even of heterogeneous vendors.

The Workshop will try to collect and analyse requirements, especially from Bioinformatics applications and propose and discuss available solutions.

For more information click here -
http://www.pi.infn.it/~pucciani/constanza/workshop/

EMBRACE WP1 (Data) and WP2 (tools) workshop June 5-7 2006
Posted on Monday, 08th May 2006

EMBRACE WP1 (Data) and WP2 (tools) workshop June 5-7 2006

The EBI (Peter Rice and Alan Bleasby) will organize a data content and analysis tools workshop at the EBI in Hinxton, Cambridge, UK. All Embrace-ers are invited to participate.

To register please contact Peter Rice (pmr@ebi.ac.uk)

There is a practical technology workshop soon after in Helsinki. Details are on the CSC website

Draft Program

Monday June 5

12:30 Arrival and Registration

13:00-14:00 Lunch

14:00-14:20 Welcome and Introduction

14:20-15:00 Partner Reports (about 20 minutes each)

15:00-15:30 Coffee

15:30-17:00 Partner Reports (about 20 minutes each)

17:00-18:30 Open Discussion

18:30 Walk to Red Lion for dinner

21:00 Bus transfer to hotels



Tuesday June 6

Data Content

9:00- 9:30 Alberto Labarga: EBI Web Services

9:30-10:00 Arek Kasprzyk: BioMart

10:00-10:30 Tom Oinn: Taverna

10:30-11:00 Chris Taylor: A Coordinated Multi-Omics View of Data Standards

11:00-11:30 Coffee

11:30-12:00 Tony Burdett: ComparaGrid

12:00-12:30 Open Discussion

12:30-13:30 Lunch

13:30-14:00 Jon Ison: Tool Definitions

14:00-14:30 Mahmut Uludag: SoapLab Future

14:30-15:00 Peter Rice: EMBOSS

15:00-15:30 Coffee

15:30-18:30 Open Discussion

18:30 Walk to Red Lion for dinner

21:00 Bus transfer to hotels

Wednesday June 7

9:00-13:00 Open Discussion

13:00-14:00 Lunch

14:00 Departure


Travel instructions
Travel instructions are available here.

Sorry, accommodation on campus is fully booked by another meeting.

there are rooms at local hotels, for example:

The Crown House Hotel
Great Chesterford
Saffron Walden
CB10 1NY
Tel +44 (0) 1799 530515 or 53025
Fax +44 (0) 1799 530683
www.thecrownhousehotel.com

Duxford Lodge Hotel (expensive)
Ickleton Road
Duxford
Cambridge
CB2 4RT
Tel: 01223 836444 Fax: 01223 832271
E-mail: admin@duxfordlodgehotel.co.uk

Travelodge Cambridge Fourwentways Hotel (budget)
A11/A1307 Fourwentways, Abington
Cambridge CB1 6AP
Tel: 0870 191 1519
Fax: 01223 839 479
online booking: http://www.travelodge.co.uk/find_a_hotel/hotel/hotel_id/19/CambridgeFour...

Details on hotels in Cambridge can be found at:
http://www.smoothhound.co.uk/cambridg.html

If you have problems finding affordable accommodation please contact the project manager, Kerstin Nyberg (knyberg@ebi.ac.uk)

TAXI:

KENWAY
Tel +44 (0) 1223 832 515

MID ANGLIA
Tel +44 (0) 1223 836 000

MASTERCAB
Tel +44 (0) 1223 566 654

Taverna workshop April 8-9 2006
Posted on Thursday, 02nd March 2006

On Saturday April 8 and Sunday April 9 the EBI (Tom Oinn) will organize a Taverna workshop at the CMBI in Nijmegen. This is the third of four train-ourselves workshops. All Embrace-ers are strongly suggested to participate (unless they already know how to work with Taverna, of course).

Over the next ten days this site will be filled with all necessary information.

Program

Saturday

  • 9:00-11:00 Seminar on Taverna
  • 11:00-11:30 Coffee
  • 11:30-13:00 Hands-on Taverna training
  • 13:00-14:00 Lunch
  • 14:00-15:30 Hands-on Taverna training
  • 15:30-16:00 Tea
  • 16:00-18:00 Hands-on Taverna training



Sunday

  • 9:00-10:00 Seminar
  • 10:00-11:00 Hands-on Taverna training
  • 11:00-11:30 Coffee
  • 11:30-13:00 Hands-on Taverna training
  • 13:00-14:00 Lunch
  • 14:00-15:00 Round table Taverna discussion
  • 15:00-15:30 Tea
  • 15:30-late Hands-on Taverna training, question session, beer, ...



Travel instructions
Travel instructions are available here.

Instructions about how to get from the hotel to the University will be available at the hotel. The hotel is Sionshof. Sionshof is on this map at the intersection of Sionsweg and the N842, the University entry is half-way the top-left corner of the "Botanische Tuin Brakkestein" and the second character "o" in Toernooiveld.
route

Financial
There will be no fees, the first 20 to sign on can stay in the (4 star ****) hotel for free (Double occupancy) and get their travel costs reimbursed. This hotel is at 25 minutes walk from the training facility. From participant 21 on, you will have to find (and pay!) your own hotel.

Other
The language of the course will be English.
Course material will be handed out at the nmeeting.
Participants

The list of participants is available here.

 

Second Annual General Meeting
Posted on Thursday, 10th February 2005

The Second Annual General Meeting will take place in Uppsala, Sweden on March 21st to 22nd.

The meeting will start at 9:00 on Tuesday 21 March, and finish at 15:00 on
Wednesday 22 March. Online registration

The first day of the meeting will consist of progress reports from the
work packages. There will a business meeting and individual work package
sessions on the morning of 22 March.
Provisional Agenda

EMBRACE Press Release
Posted on Monday, 31st January 2005

European bioinformatics grid receives ???8 million - Press Release here