GeneBio and Swiss-Prot A Love Story in 3 Acts

1. GeneBio and Swiss-ProtA Love Story in 3 Acts Nasri G. Nahas, CEO (using Ron as his mouthpiece)

2. Swiss-Prot From PIR, EMBL to… Act I: 1986 But I need a good protein db!?!? Swiss-Prot was created by Amos Bairoch and quickly became THE reference that every life scientist dealing with proteomics needed to access.

3. It looks like you should renew your battery ! Act I: 1986-1996 But life alone is sometimes tough : the Swiss-Prot financial crisis

4. Act II: 1997 • GeneBio was created by Ron Appel, Amos Bairoch and Denis Hochstrasser… • …with the initial mandate of being the commercial arm of the SIB… • … notably to distribute Swiss-Prot to the commercial community and provide sustainable funding for this precious resource… • ... but also with the objective of developing the company as a sustainable bioinformatics company.

5. Lake Geneva Region Working Closer Together

6. 1997-2004: Seven Years of Loyal Services ~750 licenses signed in total With > 400 companies worldwide

7. 1997-2004: Seven Years of Loyal Services Generating >30M CHF in cumulative revenue to SIB-EBI Mainly through Swiss-Prot

8. 2004: The end of it… for Swiss-Prot But life is also about separation: the new Swiss-Prot funding scheme.

9. Act III: 2005 And Life goes on: GeneBio’s life without Swiss-Prot. Since its inception in 1997, GeneBio has evolved from its initial, and continuing, mandate as exclusive distributor for the renowned Swiss Institute of Bioinformatics (SIB) into a truly multifaceted bioinformatics companyoffering original solutions that shape heterogeneous information into relevant biological knowledge

10. Our Vision “Everything has been thought of before, the challenge is to rethink it.” -Goethe

11. Challenge: Transforming data into knowledge today Data Knowledge 20 years ago Data Knowledge

12. Integrated and structured knowledge Data Knowledge (ctd.) Masses of heterogenous information

13. Training Services • e-Proxemis : Our bioinformatics learning portal for proteomics • Content Solutions • SIB Databases : PROSITE and SWISS-2DPAGE • Current Biodata The Next Generation of knowledge bases Our Solutions From data to knowledge… the GeneBio way • Software Platforms • Phenyx : The mass spectrometry data analysis platform • Melanie & ImageMaster™ 2D Platinum : The recognized leader in the field of 2-D gel electrophoresis • MSight: Melanie applied to LC-MS imaging Coming soon

14. 2D Image Analysis : Melanie / ImageMaster™ 2D Platinum 6.0

15. Melanie / ImageMaster 2D Platinum Background • The Melanie 2D gel analysis software is developed by the SIB and has been commercialised by GeneBio for several years • GeneBio, the SIB and Amersham Biosciences joined forces to offer the next generation of 2-D gel analysis tools: complete integration of Melanie into Amersham Biosciences’ ImageMasterplatform • ImageMaster 2D Platinum 4.9, launched in September 2003 was the first version effectively integrating Melanie • ImageMaster 2D Platinum 5.0, ensuring integration with Amersham Biosciences equipment, was released in January 2004 • ImageMaster 2D Platinum 6.0, fully supporting the DIGE technology, became available in August 2005 from GE Healthcare (formerly Amersham Biosciences)

16. Melanie / ImageMaster 2D Platinum The Product A powerful software application for the analysis of 2D gel images: • Manages both conventional 2-DE and DIGE gels following exactly the same workflow. • Accurately and rapidly identifies and quantifies your spots, matches your gel images, and finds significant protein expression changes. • Offers numerous filtering, querying, reporting, statistical and graphing options so that you can easily view, compare, analyse and present your results. • From the raw experimental images to the preparation of a publication, it takes you successfully through each stage of a gel study.

17. Phenyx is a software platform dedicated to the identification and characterization of proteins and peptides from mass spectrometry data • Developed by GeneBio, in collaboration with the SIB • Launched in September 2004 (version 1.8) : • Version 1.9 in September 2005 • Version 2.0 in February 2006 • Version 2.1 in May 2006

18. Phenyx Key Features • Robust and flexible scoring (incorporates the true probabilistic and flexible scoring system OLAV • takes into account several quantitative & structural information • Can be optimized for each instrument / lab pipeline • validated in an industrial high-throughput environment, running on 1,400 processors. • Flexible and interactive interface: the “Phenyx Web Interface” (PWI) • Enhanced accuracy and reliability thanks to the “manual validation” functionality and the unique automatic “conflict resolution” algorithm. • Extensive use of annotations in databases (PTMs, variants, AA modifs…) • Combination/cross-validation of results via the “results comparison tool” • Integration of Phenyx into workflows (LIMS systems…) without a glitch ( battery of Perl scripts, Perl modules, XML result files, command line interface…)

19. A protein-centric summary A central Desktop A spectrum-centric summary A peptide match detail A result comparison A protein match detail The Phenyx Web Interface (PWI): One Result, Multiple Views

20. Time 0 10 20 30 40 m/z 600 800 400 1000 1200 20 min 200 Da Platform Integration LC-MS analysis Annotated images Raw LC-MS Exported peptide identifications Phenyx visualisation Peaklists

21. Bioinformatics learning portal for Proteomics

22. http://access.e-proxemis.com e-Proxemis : The Concept • A bioinformatics learning portal for proteomics • Refinement of the successful Proxemis (classroom) course • Our goal : To give life scientists the bioinformatics background they need through a self-learning platform that mirrors real-world situations with dynamic content

23. An Extended Networking Strategy Strategic Partners Distribution Partners Academic Partners