SME Bioinformatics Forum, Munich


  Monday 18 October 2010

Registration closed


Support for Industry is part of the mission of the EMBL-European Bioinformatics Institute. To this end we have established an annual series of information workshops based in differing locations in Europe. These workshops are designed to allow SMEs to hear about data resources, tools and services that are provided freely by EMBL-EBI and our collaborators, this year with a special focus on the European Patent Office (EPO).
The workshop will provide the opportunity to introduce the tools and data resources that are available and the opportunities for SMEs to use and integrate these resources in order to derive business benefit from the existing and developing infrastructure.
The topics of the workshop have been specifically selected on the basis of previous interactions with SMEs and include chemogenomics, cheminformatics, proteomics, text mining, literature services and analysis, web services, which is fast developing as the accepted technology in scientific computing, and patent services providing by EMBL-EBI and the European Patent Office.
This year in addition to the presentations, discussion and networking opportunities, there will also be an opportunity for some hands-on tutorials at the offices of the EPO. In order to encourage participation, the registration costs for the workshop (50 Pounds per participant) have been highly subsidised through the generous contributions of the hosting organisations (BioM and the EPO) and financial contributions from a number of EU projects (ENFIN, SLING, CALBC and ELIXIR) that are coordinated by EMBL-EBI and are targeted to provide bioinformatics tools and data resources for European research.

Additional information

Hotel recommendations

Hotel where speakers are staying
Falkenturm Hotel
Falkenturmstrasse 3
80331 Munich

Additional hotel recommendations (close to EPO):
- Jedermann
- Europe Hotel Senator
- Four Points by Sheraton
- Motel One
- Sofitel Bayerpost
- Citadines Arnulfpark



Monday, 18th October 2010 (Offices of BioM, Munich)
12:00-12:40 Registration and Refreshments
12:40-12:50 Welcome (Horst Domdey, BioM)
12:50-12:55 Meeting Overview (Dominic Clark & Pascal Kahlem, EMBL-EBI)
12:55-13:10 Overview of EMBL-EBI data resources and services
(Dominic Clark, EMBL-EBI)
13:10-13:40 EMBL-EBI Proteomics data resources and services
(Rafael Jimenez, EMBL-EBI)
13:40-14:10 ENFIN - EnVISION and DAS
(Rafael Jimenez, EMBL-EBI)
14:10-14:40 Cheminformatics resources and services at EBI
(Chris Steinbeck, EMBL-EBI)
14:40-15:10 Coffee Break
15:10-15:40 Using Web services in Your Data Analysis Pipeline
(Erik Bongcam-Rudloff, Uppsala University)
15:40-16:10 Web Services: The Biocatalogue Project
(Eric Nzuobontane, EMBL-EBI)
16:10-16:40 ChEMBL databases and tools: Supportof target selection and validation
(John Overington, EMBL-EBI)
16:40-17:00 Short Break
17:00-17:15 Presentations from Regional Organisation
(Introduced by Mathias Lamparter, BioM)
17:15-17:45 Knowledge Management for Scientific Intelligence with BioXM
(Klaus Heumann, CEO, Biomax Informatics AG, BioMax Informatics AG, Munich,
17:45-18:15 m>Presentation from Dr. Martin Seifert, Vice President Business Development and Consulting, Genomatix Software GmbH.
18:15-18:25 Closing Comments
(Mathias Lamparter, BioM)
18:25-18:35 Closing Comments
(Dominic Clark & Pascal Kahlem, EMBL-EBI)
18:35 Networking Buffet Supper


Tuesday, 19th October 2010 (European Patent Office, Grasserstr 2, room 8661)
08:45-09:00 Coffee
09:00-09:10 Welcome (Noël Campling, Director of Know-How, EPO)
Introduction to the second day (Dominic Clark, EMBL-EBI)
09:10-09:40 EMBL-EBI Literature Services and Applications
(Jo McEntyre, Head of Literature Services, EMBL-EBI)
09:40-10:10 EMBL-EBI text mining tools and mapping of targets/pathways to disease
(Dietrich Rebholz-Schuhmann, EMBL-EBI)
10:10-10:35 EMBL-EBI Patent related services
(Jennifer McDowall, EMBL-EBI)
10:35-11:00 Coffee Break
11:00-11:15 EPO Services, resources for SMEs and the SLING project
(Stephane Nauche, European Patent Office)
11:15-11:45 Patent Information: esp@cenet (
(David Evans, European Patent Office, Munich)
11:45-12:15 How the EPO searches prior art in Biotech; European Patent Academy and dissemination of knowledge
(Titus Vogt, European Patent Office)
12:15-13:00 Biotech patentability
(Titus Vogt, European Patent Office, Munich)
13:00-13:15 Wrap up of second morning including Panel Q&A
(Pascal Kahlem EMBL-EBI)
13:15-14:30 Lunch
14:30-15:30 Hands-on workshops (EPO training rooms 1909 & 1910, Bayerstr 115). Limited Availability.
Workshop A: EMBL-EBI resources (Jennifer McDowall, EMBL-EBI)
Workshop B: EPO resources (David Evans, European Patent Office, Munich)
15:30-15:45 Break
15:45-16:45 Hands-on workshops (EPO training rooms 1909 & 1910, Bayerstr 115). Limited Availability.
Workshop A: EPO resources (David Evans, European Patent Office, Munich)
Workshop B: EMBL-EBI resources (Jennifer McDowall, EMBL-EBI)
16:45-17:00 Wind down cocktail & feedback discussion
17:30 Close of day

Contents of the EPO Resources workshop:

  • The basics of how to use the public patent database: espacenet -
  • How to use patent classification codes (IPC & ECLA) for more targeted searching
  • How to interpret the search results; how to "read" a patent; how to use the search report on a patent for further leads
  • How to use espacenet to find collaborators and partners
  • How to monitor a pending application of interest in Register Plus -
  • How to use INPADOC to check the status of a patent (has it lapsed? is it in force in a particular country?)


Meeting location

First day - BioM Biotech Cluster Development GmbH (A)
Am Klopferspitz 19, 82152 Martinsried - Germany. Directions.

Second day - European Patent Office (B)
Grasserstr 2, 80335 Munich - Germany
The morning plenary will be in the building flanked by Grasser Str; the afternoon workshops will be in the building opposite, on the south side of Bayerstr. Trams 18 & 19 run along Bayerstr; the S-bahn station at Hackerbruecke is immediately to the north. Hackerbruecke is one S-bahn stop west of the main train station (Hauptbahnhof); three stops west of Marienplatz (town centre).