EMBRACE outreach activities at CBS

Past activities

• Workshop for Web Service Providers in Bioinformatics: Syntax, Semantics and Publishing, CBS, June 2-4, 2010
  The workshop introduced comprehensive guidelines for design, semantic annotation and publishing of SOAP-based Web Services in the area of life sciences. It was expected that the participants should be familiar with the basic concepts of Web Services, and should preferably already have produced or have been involved in the production of one or more such services.
  The emerging EMBRACE Guidelines for Web Service providers were discussed in detail. The following issues of key importance to Web Service interoperability, easiness of use and visibility to the community were then covered in depth: use of externally defined data types (example: BioXSD), semantic annotation (example: EDAM) and publishing (example: BioCatalogue).
  All the points above were illustrated with hands-on exercises. They were performed on the participants' own Web Services. Thus, each participant should have remote access to his/her own Web Service generation workbench. Windows laptops with SSH and X11 were provided on request.

• Workshop on Perl, SQL and Web Services, CBS, November 16-20, 2009
  The workshop was 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 covered a general-purpose scripting language (Perl), database manipulation (SQL) and programmatic access to remote resources (Web Services). Brief introductory lectures were followed by extensive hands-on exercises aiming at the ability to develop clean, efficient Perl scripts accessing relational databases and remote resources. There were template scripts available to take home and develop further in the context of the participant's own work.

• Workshop on Client Side Scripting for Web Services, CBS, February 6-8, 2008
  The workshop focused on practical use of Web Services in scripts/programs developed on the client's own computer. It was built around the hands-on exercises; existing EMBRACE Web Services were used to construct workflows. Interoperability was the key issue. In the last exercise there was time reserved for work with the Web Services of interest to the participants. The workshop home page remains online for reference; the programme contains links to the lecture notes, exercise cookbooks and example solutions to problems etc.

• Workshop on Modern computer tools for the biosciences, Uppsala, Sweden, March 22-23, 2007
  The workshop was organised by Swedish University of Agricultural Sciences (SLU, EMBRACE partner 6). CBS contributed with two presentations, both reporting our work on Web Services:
  • Implementation of Web Services for bioinformatics - challenges, decisions, experiences, Peter Fischer Hallin
  • Using Web Services in bioinformatics: converting remote services into local utilities, Francisco Roque

• Workshop on Bioinformatics of Immunology, CBS, January 24-26, 2007
  The workshop addressed the current issues in immunobioinformatics. It consisted of lectures and hands-on computer exercises, where the participants were introduced to a range of computational methods used in the field and to a selection of relevant services available on the Internet. Special attention was given to SOAP based Web Services. The workshop home page remains online for reference; the programme contains links to the lecture notes, exercise cookbooks and example solutions to problems etc.