Name: Dr. Werner Van Belle
e-mail: werner@sigtrans.org, werner.van.belle@gmail.com
Webpage: http://werner.sigtrans.org/
Address: Entenweidstrasse 4, CH-4056 Basel, Switzerland
Phone: Work: (+41) 61 387 31 91
Date of birth: 21 June 1975
Place of birth: Anderlecht, Belgium
Nationality: Belgian
Marital Status: Not married
Military Service: None; not obligatory in Belgium since
1975
Drivers License: B (cars and small motorcycles). No practice
since 1995
Languages: Dutch & English
My expertise lies in three distinct areas: a) bioinformatics (detailed in section 4.1.4, 4.1.2, 4.1.3 & 4.1.1), b) signal processing (detailed in section 4.2.1, 4.2.2, 4.1.4 & 4.1.3) and c) distributed systems (detailed in section 4.3.4, 4.3.3, 4.3.2 & 4.3.1);. My education summarized by the dissertations,
| Employer | Group | Position | Start Date  End Date |
Time
VUB |
Abbreviations: VUB = Vrije Universiteit Brussel (Brussels University); UiTø = University of Tromsø; UNN = University Hospital of Northern Norway; BSSE = Department for Biosystems Science and Engineering
From March 2008 to March 2009 I was responsible for setting up a primary analysis pipeline for the Deep Sequencing Facility in Basel. This included various aspects among which understanding the Illumina software but also administrative issues such as sample tracking and data delivery. In the end, this project was at an impasse. With on one side an IT department that refused to do what we needed (making backups, installing web servers and installing databases was 'not their job') and on another side a research department that did not see the need for an official software project because they did not want to understand the basic steps of software engineering: requirement analysis, system design, implementation, validation etc. This part of the work was highly unrewarding, even to the point that I left the DBSSE entirely.
A second aspect of my work at DBSSE was research on how to analyze genomic signal track and how to find useful relations between these tracks. To this end I tested a number of novel approaches on Human Histone Methylation and Acetylation patterns. This was very interesting and offered a number of novel insights.
In connection with the Virology department of the University Of Tromso, I investigated the measurement accuracy of the microarray facility. This resulted in the development of a new technique in which confidence intervals on all the measured dots are reported. This information was further used to integrate a protein interaction map and predict which proteins are likely influenced by/will likely influence MK5.
In connection with Haukeland University Hospital (Bergen) we investigated P53 (a protein related to cell life and death and its gene is often mutated in cancer). We received bio-signatures of P53 expression for various leukemia patients and got the challenge to analyse these. First we needed to remove various artifacts from the images, including camera geometry artifacts, washing and drying effects, scratches, bubbles, light conditions and translational, rotational and zooming variances. In this research we developed a novel denoising technique. Afterwards, alignment was necessary and the analysis of the actual data. This led to a novel analysis technique that is being patented.
MALDI-TOF mass spectrometry is a well known and widely used technique to fingerprint and sequence proteins. However widely used, the signal output of these machines often contain disturbing artifacts such as static tones, linearly up-sweeping tones, exponentially decaying tones and probabilistic pulse trains. Their presence reduces the accuracy of peak localization and might introduce phantom peaks. This further complicates a) automatic selection of peaks, b) makes it impossible to normalize mass spectrogram's and c) in general reduces the performance of high throughput proteomics. We developed a) a number of specialized algorithms to remove these artifacts, based on wavelets, and b) a number of techniques to automatically assign confidence scores to peaks, based on auto-correlation techniques and machine modelling. The combination of the presented techniques allow for an accurate and automated sample analysis, which in turn helps in the determination of the sample content.
In 2001 I created a fully automatic BPM counter to measure the tempo of music. This is done by autocorrelation, which in itself is not a new technique, however at that moment the use of this technique to measure the tempo was entirely new. Over the years this program has been extended to recognize sound spectra, rhythmical information, ambiance and compositional information. This allows the program to automatically select matching songs, cluster them and visualize them using a PCA analysis. More information can be found at http://bpmdj.sourceforge.net/. The current modules include
Tempo module - Five different tempo measurement techniques are available of which auto-correlation and ray-shooting are most appropriate. All analyzers in BpmDj make use of the Bark psycho-acoustic scale. The spectrum or sound color is visualized as a 3 channel color (red/green/blue) based on a Karhunen-Loéve transform of the available songs.
Echo/delay Modules - Measuring the echo characteristics is based on a distribution analysis of the frequency content of the music and then enhancing it using a differential auto-correlation.
Rhythm/composition modules - Rhythm and composition properties
rely on correct tempo information. Rhythm relies on cross correlation
and overlaying of all available measures. Composition relies on measuring
the probability of a composition change after 
measures.
From an end-user point of view the program supports distributed analysis, automatic mixing of music, distance metrics for all analyzers as well as clustering and automatic classification based on this information. Everything is tied together in a Qt based user interface.
Cryosleep is a program that generates soothing brainwaves relying on the bi-aural effect. I developed this from 2003 to 2005 and has proven to be a very popular download. The value of the program comes both from its unique noise shaped frequency spectrum (the sounds are very 'friendly' to listen to) and its free availability at http://werner.onlinux.be/Cryosleep. Cryosleep relies on a power-law to alternate the composition and on the bark psycho-acoustic scale for frequency selection.
In 2006 I became involved with ship to shore protocols -or- how to solve very practical network problems with the following requirements: a) the off-boat interface can change at any time, but the internal network needs to stay fully connected b) how to bring up/down outgoing links; c) how to control incoming and outgoing connections based on current cost-rate and d) how to install a least cost routing engine on such a router ? To approach this problem we investigated NuFw, IPv6 and Mobile IP.
From 2001 to 2003 I wrote my PhD, a monograph titled ``Creation of an Intelligent Concurrency Adaptor in order to mediate the Differences between Conflicting Concurrency Interfaces''. It contained 14 distinct chapters, of which 10 standing independent. The full text is available on my homepage. In summary, I investigated a particular problem of open distributed systems namely: concurrency management between components written by different manufacturers. All too often, the concurrency-strategy provided or required by a component is badly documented and rarely matches the concurrency strategy provided or required by other components. Whenever this happens there is a concurrency interface conflict. Solving such conflicts can require a substantial amount of manpower, especially because in open distributed systems components can be updated without prior notification and without guarantees that new interfaces are backward compatible. Concurrency behavior modifications can range from syntactic modifications over slight semantic differences to completely new concurrency strategies. For example, changing a nested locking strategy to a non-nested locking strategy or changing a non-blocking server to work in a blocking manner.
I approached the presented problem by automatically generating a concurrency interface adaptor between various provided an required concurrency behaviors. This process required the formal documentation of the involved concurrency interface by means of colored Petri-nets. Once these are available, a concurrency adaptor is deployed in two stages. The first stage learns how to reach various check points in both the server code and client code, thereby bypassing the concurrency behavior entirely. Then the second stage observe the requested state in the client and realizes it in the server by linking together the common functional Petri-net places (a functional place is one not related to the concurrency strategy).
I have been fully involved in the SEESCOA project, which stands for ``Software Engineering for Embedded Systems using a Component Oriented Approach''. The project ran from October 1999 till September 2003. 4 academic partners were involved: 1) the VUB (Vrije Universiteit Brussel) with PROG ('Programming Technology Lab') and SELL (Laboratory for Software engineering). 2) the PARIS research group of the RUG ('Rijks Univeristeit Gent'). 3) the DISTRINET research group of the KUL (Katholieke Universiteit Leuven) and 4) the EDM Research group ('Expertise for digital media') of the LUC ('Limburgs Universitair Centrum').
The IWT funded the main chunk of the project with 2 mil EUR. 6 industrial partners were involved. These were: Siemens, Barco-Graphics, Agfa Gevaert, Imec, Philips and Alcatel. Key points of this period:
During 4 years I've been the creator and maintainer of the Borg mobile multi agent system. We viewed a mobile multi-agent as a standalone component that can communicate with other agents and migrate between places (processors). Our research aimed to conceive a distributed system and language that would allow the development of such mobile agents, without presenting the agent programmer with non functional aspects such as connection establishment, fault tolerance and so on.
During this time I researched which distribution aspects one can hide (at an acceptable price) and which ones not. In the end we were able to shield the programmer from finding the communication partners. We provided transparent communication, location transparent migration and transparent replication. We were unable to hide concurrency management (due to its inherent complexity). Therefore we developed a set of control flow modules that abstrahate around typical usage scenarios (whiteboard communication, one-to-many, many-to-one and voting patterns). Later on, this led to the applicability of Petri-nets as a modeling technique.
The Borg mobile multi agent system uses the educational language Pico as its basis. It was developed by my former adviser and due its proper memory and stack discipline enabled strong migration already in 1998. Key-points of this period:
* is the corresponding author. 
are equal contributors.
The publications and presentations below only include those related to bioinformatics. See the full length CV for a complete overview. The file CV-bio-abstracts includes the abstracts.
1. Nancy Gerits
, Werner Van Belle, Ugo Moens; Transgenic mice expressing constitutive active MAPKAPK5 display gender-dependent differences in exploration and activity; Behavioral and Brain Functions; Biomed Central; Editor(s) Terje Sagvolden; volume 3; nr 58; November 2007
2. Werner Van Belle
, Nancy Gerits, Kirsti Jakobsen, Vigdis Brox, Marijke Van Ghelue, Ugo Moens; Confidence Intervals on Microarray Measurement of Differentially Expressed Genes: A Case Study on the effects of MK5, TAF4 and FKRP on the transcriptome; Gene Regulation and Systems Biology; Libertas Academus Press; nr 1; pages 57-72; May 2007
3. Werner Van Belle
, Gry Sjøholt, Nina Ånensen, Kjell-Arild Høgda, Bjørn Tore Gjertsen; Adaptive contrast enhancement of two-dimensional electrophoretic protein gel images facilitates visualization, orientation and alignment; Electrophoresis; Wiley Interscience Vch; volume 27; nr 20; pages 4086-4095; October 2006
4. Nina Ånensen, Ingvild Haaland, Clive D'Santos, Werner Van Belle, Bjørn Tore Gjertsen
; Proteomics of p53 in Diagnostics and Therapy of Acute Myeloid Leukemia; Current Pharmaceutical Biotechnology; Bentham Science Publishers Ltd.; volume 7; nr 3; July 2006
5. Werner Van Belle
, Nina Ånensen, Ingvild Haaland, Oystein Bruserud, Kjell-Arild Høgda, Bjørn Tore Gjertsen; Correlation analysis of two-dimensional gel electrophoretic protein patterns and biological variables; BMC Bioinformatics; volume 7; nr 198; April 2006
6. Werner Van Belle
, Bjørn Tore Gjertsen; Correlation Determination System: P53 Correlations; Submitted as a patent application; Editor(s) Frank B. Dehn; April 2006
7. Werner Van Belle
, Olav Mjaavatten; Artefacts in the Mass Spectra Output from MALDI-TOF and MALDI-TOF/TOF Machines; Proceeding of the VIIth International Symposium of the Protein Society section proteomics, interactomics and protein networks; April 2005
8. Werner Van Belle
, Tom Mens, Theo D'Hondt; Using Genetic Programming to Generate Protocol Adaptors for Interprocess Communication; Evolvable Systems: From Biology to Hardware, Proceedings of the 5th Intl. Conference on Evolvable Systems (ICES2003); Springer Verlag: Lecture Notes in Computer Science (LNCS 2606); Editor(s) Andy M. Tyrrel and Pauline C. Haddow and Jim Torresen; pages 422-433; March 2003
1. Werner Van Belle
; (Ortholog) Mapping the Applied Biosystems Human/Mouse Survey v2.0 Micro-arrays to Ensembl Gene Identifiers; Bioinformatics; Yellowcouch Scientific; 23 pages; May 2007
1. Reanalysis of Histone Methylation and Acetylation Patterns; presented at ETH Zurich, Department of Biosystems Science and Engineering, Research Seminars, Switzerland, December 2008; Friedrich Miescher Institute (FMI) Computational Biology Seminars, Switzerland, December 2008
2. Sequencing by synthesis: from samples to data patterns.; presented at Novartis; Quantitative Biology Meetings, Switzerland, November 2008
3. A Whole-genome RNAi Screen Identifies Novel Regulators of Notch Signaling in Drosophila melanogaster; presented at ETH Zurich Departmental Retreat Bad Zurzach, Switzerland, October 2008
4. Deep Sequencing; presented at 1st workshop on high throughput sequencing; ETH Zurich in Basel, Switzerland, October 2008; All Systems X day, Switzerland, October 2008; ETH Zurich Departmental Retreat Bad Zurzach, Switzerland, October 2008
5. Modulation of p53 protein isoforms and their function in acute myeloid leukaemia; presented at FEBS Meeting Oslo, Norway, October 2008
6. Primary Analysis: From Sample to Wig file in 8 Easy Steps; presented at 1st workshop on high throughput sequencing, Switzerland, October 2008
7. The Illumina GA II Sequencing System; presented at Department of Computer Science; ETH Zurich; Zurich, Switzerland, October 2008
8. What happened to my data. Screening a mutal stabilized reporter system.; presented at ETH Zurich, Department of Biosystems Science and Engineering, Research Seminars, Switzerland, August 2008
9. Deep Sequencing Unit: Inputs, Outputs, File Sizes & Formats; presented at ETH Zurich in Basel, Switzerland, July 2008
10. Deep Sequencing Unit: Information Infrastructure; presented at ETH Zurich in Basel, Switzerland, April 2008
11. Biological Networks and Noise Propagation; presented at ETH Zurich in Basel, Switzerland, January 2008
12. 2D Gel Correlation Analysis and Perspectives on Systems Biology; presented at Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland, October 2007
13. Microarrays, Protein Interaction Maps and Elevated Mazes; presented at Animal Sciences Group, Wagingen Universiteit, Lelystad, The Netherlands, September 2007
14. Micro-Array Confidence Intervals: a more detailed look & Protein Interaction Map Integration & Visualization; presented at Medical Genetics, University Hospital Northern Norway, Tromso, Norway, April 2007
15. Close-to-the-experiment Data Analysis; presented at LabForum, University Hospital Tromso (UNN), Norway, March 2007
16. Correlation Analysis 2D Gels; presented at the High Technology Center of Bergen, Norway, February 2007
17. Micro Array Error Analysis and Integration/Visualisation of a Protein Interaction Map; presented at the Department Virology, University of Tromso and LabForum, University of Tromso & University Hospital of Tromso, Norway, January 2007
18. Systems Biology: Bridging the gap between experiment and interpretation; presented at Norut IT, Tromso, Norway, March 2006; the Institute of Biology, University of Tromso, Norway, February 2006; the Institute of Molecular Biology, University of Tromso, Norway, January 2006
19. Biological Systems: Bridging the gap between experiments and interpretation; presented at the Functional Proteomics Unit, Departement of Medical Protein research, Flemish Institute for Biotechnology (VIB), Gent, Belgium, September 2005
20. On the need for robust techniques; presented at the Department of Economic Sciences, University Leuven, Belgium, September 2005
21. Mk5 Cell Cycle Analysis; presented at the Department Virology, Institute Molecular Biology, University Of Tromso, Norway, August 2005
22. Analysis of wild type P53 protein distribution in cancer cells; presented at the 6th Bergen Conference on Cancer Research 2005 (BCCR2005) section: proteomics in cancer , Norway, May 2005
23. Denoising of MALDI-TOF Mass Spectra; presented at AOPC2005, The VIIth European Symposium of the Protein Society, section proteomics, interactomics and protein networks, Barcelona, Spain, May 2005; the Computational Biology Unit (CBU), Bergen, Norway, August 2004
24. Denoising of Maldi-Tof Mass Spectra & denoising of 2D gels; presented at the Programming Technology Lab, Computer Science Department, Vrije Universiteit Brussel, Belgium, April 2005
25. P53 Image Denoising; presented at Norut IT as part of a project delivarable in cooperation with the Hematyology Section, University Bergen, Norway, February 2005
26. Envision Software Package for the Concerted Study of Biological Data; presented at NBS 2005 (Poster), Tromso, Norway, January 2005; at Bioprosp 2004 (poster), Tromso, Norway, November 2004
27. Overview of Bioinformatics at Norut IT; presented at the Veterinaer Institute, Tromso, Norway, December 2004
28. Biological Systems, Modeling & Simulation; presented at PROBE, the proteomics unit in Bergen, Norway, August 2004; Norut IT, Tromso, Norway, August 2004
29. Automatic Generation of Concurrency Adaptors for Multi Agents; presented at the International Conference on Evolvable Systems 2003 (ICES03), Trondheim, Norway, March 2003
1. Theory and Exercises 'Concurrent Systems' - given at the VUB, academic year 2000-2001 for Franklin Vermeulen, aimed at the 3th year computer science, Vesalius college.
2. Exercises 'theory of database systems' - given at the VUB, academic year 1998-1999 for Robert Meersman, aimed at the 3th year of computer science.
3. Exercises 'Graphics' - given at the VUB, academic years 1998-2000 (2), for Theo D'Hondt, as an optional course in the 2nd cycle of the computer science curriculum.
4. Exercises 'Algorithms and Data Structures' - given at the VUB, academic year 1998-1999 (1), for Theo D'Hondt, aimed at the 2nd year computer science.
5. Exercises 'Distributed Systems' - given at the VUB, academic years 1998-2003 (5), for Marnix Goossens, aimed at the 2nd cycle of the standard computer science curriculum, the 2nd cycle of the applied computer science curriculum and the 3th year in teleinformatics.
6. Project guidance for a computer science course on Systems - given at ETH Zü rich, for Nessime Tatbul in conjunction with Nihal Dindar.
1. User Interface for Mobile Agent; Tan Jiaming; 1997-1998
2. Print Spooling: a Critical Approach Toward a Specific Problem in a Hybrid Environment; Dominique Kindt; 1997-1998
3.* A Critical Evaluation of Distributed Collaborative Computer Applications; Stefan Van de Velde; 1997-1998
4.* A Study of Communication Models for Mobile Multi Agent Systems; Karsten Verelst; 1998-1999
5. Combining Components using Control Flow Components; Philippe Demaecker; 1999-2000
6. Applicability of Mobility, a Case Study; Frederick Nyssens; 2000-2001
7.* Shagger: a Distributed File Sharing Community with Transparent User Management and Adaptive Replication; Wim Boffe; 2000-2001
8.** A Strategy to Generate a Scheduler for Time Critical Programs by means of Finite State Machines; Jessie Dedecker; 2000-2001
9. Applications for Code Mobility on Handheld Devices; Enzhen Luo; 2000-2001
10. Synchronisation & Communication in Mobile Multi Agents Systems: CSP Revisited; Jannes Pockele; 2000-2001
11.* Using a Declarative Language to support Concurrency Management in Mobile Multi Agent Systems; Kristof Van Buggenhout; 2000-2002
12. Quality of Service for Mobile Multi Agent Systems; Cedric Van Rykel; 2001-2002
13. Reflection by means of JIT compilation; Paul Henri van der Steichel; 2001-2002
14. Distributed Application Serving using Mobile Agents; Koen Bailleul; 2001-2002
15.* Transparent Fault Tolerance for Mobile Multi Agent Systems; Pieter Verheyden; 2001-2002
16. [Sensor only] Distributed Transaction Management - A Simulation; Weihai Pan; 12 Dec 2004; Computer Science Department, Universiyt Tromso
1. Modularizing Advanced Transaction Management; Tackling Tangled Aspect Code; Johan Fabry
2. Jessie Dedecker with his Phd on Pervasive Applications
Jury Member for CETRIL (Centre Européen de Transfert et de Recherche en Informatique Libre) in 2006.
Operating Systems: MSDOS, MS Windows (3.11, 95, 98, NT), Linux (Slackware, Debian, Gentoo), Solaris & SunOS
Programming Languages: Python, Jython, C, C++, Pascal, Prolog, Lisp, Scheme, Java (1.1.2, 1.1.8, 1.3.1, 1.4.0, 1.4.1), Pico, Borg; Libraries: QT, MFC,...
Middleware: OrbixWeb, Aglets, Voyager,...
Databases: MSAccess, MySQL, PostgressSQL...
Methodologies: UML (MSC's), OMT, Petri-Net Modelling, Room, Real-Time UML...
From November 1995 till December 1997 I was a board member of the student organization 'Infogroup'. This internal VUB organization was responsible for maintaining the computer rooms available to students, distributing course notes and maintaining a library of computer science books. I was active as system administrator and course manager. Key-points of this period:
The Programming Technology Lab of the VUB was responsible for the
organization of ECOOP'98, a well known conference on software engineering
by means of objects/aspects/components. I've been responsible for
the setup and maintenance of the visitors computer rooms.