The VSNS BioComputing Division

Our 1995 and 1996 courses received the ``Special Prize on Distance Training'' , awarded during the ``Multimedia Transfer '97'' competition which was part of the ``Learntec '97'' fair. We're planning a new course in 1998, using revised material.

Our ``Biocomputing For Everyone !'' WWW Pages have been a finalist in the Pirelli INTERNETional Award, and our ``Biocomputing For Schools'' WWW Pages have been in the final round of the Second European competition for educational multimedia for schools. The ``Internet Biologists'' project can be seen as another spin-off, together with local courses, and the ``Bioperl'' project.

We're currently setting up a virtual Study Project Agency, which initiates joint projects between bioinformatics students and researchers from all over the world. At the moment, brokering is restricted as a service for second year graduates in the Bielefeld bioinformatics curriculum.

Via computer networks, we are able to offer our material free of charge to a worldwide audience. The VSNS BioComputing Division is an interdisciplinary effort coordinated by Robert Giegerich and Georg Fuellen, now involving more than 50 researchers and consultants from academia and industry. It serves as a test-bed for virtual collaboration among scientists, using a minimum of technical and financial resources to achieve maximum service to the scientific community.

On this page, past and present collaborators can present short descriptions of their affiliations and interests.

See also the List of Contributors to our ``Biocomputing for Everyone !'' WWW pages.

List of Collaborators

• Wolfram Altenhofen, Ludwigshafen, Germany. Instructor.
  His BioMOO character is WolframA. Email: wolfram.altenhofen@zhv.x400.basf-ag.de

  Dr. Wolfram Altenhofen is a PostDoc at the Drug Design research group of the BASF AG, Ludwigshafen, Germany. He is interested in characterizing ligand-receptor interactions using biophysical and molecular biology methods as well as computer modelling.

• Andreas Dress, Bielefeld, Germany. Author of the course material on Mathematical Analysis of Sequence Data.
  Email: dress@mathematik.uni-bielefeld.de.

  Prof. Dr. Andreas Dress heads the RCSF - Research Center for Studies on Structure Formation at the University of Bielefeld. His main research areas are equivariant combinatorics, combinatorial geometry, and applications of discrete mathematics in the life sciences and in chemistry.

• Georg Fuellen, Bielefeld, Germany. Author of the course material on Multiple Alignment. Course Coordinator.
  His BioMOO character is GeorgF. Email: fuellen@techfak.uni-bielefeld.de, fuellen@Techfak.Uni-Bielefeld.DE.

  Georg Fuellen is a PhD student at the Research Group in Practical Computer Science, Department of Computer Science and Biotechnology, University of Bielefeld. He is investigating methods for identifying phylogenetic information, and thereby improving multiple alignments.

• Robert Giegerich, Bielefeld, Germany. Co-author of the course material on Pairwise Alignment and Similarity. Course Coordinator.
  His BioMOO character is RobertGi. Email: robert@techfak.uni-bielefeld.de.

  Prof. Dr. Robert Giegerich teaches programming languages, compiler construction and sequence analysis algorithms at the University of Bielefeld, Germany. He is also in charge of the new curriculum in Bioinformatics at Bielefeld University. His research interests include methods for approximate matching of complex structural patterns.

• Gustavo Glusman, Weizmann Institute, Israel. ''Archwizard'' of BioMOO, where the courses take place.
  His BioMOO character is Gustavo. Email: Gustavo@bioinformatics.weizmann.ac.il.

  Gustavo Glusman is a biologist at the Weizmann Institute of Science, Rehovot, IL with a wide background in computing. He is a VSNS-Organizer, wizard of BioMOO, a virtual meeting place for biologists and teaching site of GNA-VSNS, and a technical advisor to the GNA.

• Brian Golding, McMaster University, Canada. Instructor (in 1995 only).
  His BioMOO character is BrianG. Email: Golding@McMaster.ca.

  Dr Brian Golding is a faculty member in the Department of Biology, McMaster University, Hamilton, Ontario, Canada L8S 4K1. He has interests in molecular evolution and in population genetics. This particularly includes the effects of natural selection on sequences and the patterns of spontaneous mutation/substitution.

• Chin Hoon Lau, Singapore. Coordinator of "Bioscience Resources on the Internet".
  His BioMOO character is HoonL. Email: gclaus@pop12.jaring.my

  Chin Hoon Lau is an Honorary secretary of the Singapore Society for Biochemistry and Molecular Biology which initiated the "Bioscience Resources on the Internet" course, and a Council member of the Singapore National Academy of Science (96/97). He is interested in the utility of Internet and Bioinformatics in research and teaching. Visiting from Malaysia, he is keen in observing the development of science in South East Asia. Chin Hoon was a student of the Biocomputing Course Class of '96, and wrote a section for the "Biocomputing for Everyone" project.

• Rebecca Parsons, University of Central Florida, Orlando. Instructor.
  Her BioMOO character is RebeccaP. Email:rebecca@cs.ucf.edu.

  Dr. Rebecca Parsons is an Assistant Professor of Computer Science at the University of Central Florida, in Orlando, where she teaches programming languages, compilers and program analyis. Additionally, she is teaching a survey seminar course on Computational Biology, focusing on algorithms in the area of DNA sequence analysis, image analysis, biological modeling, and protein structure.

• Steffen Schulze-Kremer, Max-Planck-Institut fuer Molekulare Genetik, Berlin, Germany. Author of the course material on Protein Folding (teaser chapter).
  His GNA-Lab character is SteffenSK. Email: steffen@chemie.fu-berlin.de.

  Dr Steffen Schulze-Kremer is devoted to what he calls "Molecular Bioinformatics", ie. the application of sophisticated algorithms (esp. those derived from nature itself) to tricky problems in and around biosciences. Trained as a biochemist and computer scientist, among other things, he is fellow of four scholarships, lecturer at the Free University Berlin and author of two books on "Molecular Bioinformatics". He also guided a number of industrial R&D projects in this area.

• David Steffen, Baylor College of Medicine, Texas, USA. Author of the course material on Networking, and the Introduction.
  His BioMOO character is DSteffen. Email: steffen@bcm.tmc.edu.

  Prof. David Steffen PhD is President of C/Si Consulting, a company providing powerful, easy to use computing solutions to the biomedical research and clinical communities. He teaches database theory and practice at Baylor College of Medicine and works on biomedical and clinical databases. He is the author of the Tumor Gene Database at Baylor.

• Paul St. Amand, Manhattan KS, USDA Research Geneticist (Plants). Instructor.
  His BioMOO character is PaulSt. Email: PSt@KSU.KSU.Edu.

  Dr. St. Amand is a Post Doctoral researcher at the United States Department of Agriculture (USDA) at Kansas State University. His current project is modeling the rate of transgene escape from plants via pollen. His main areas of research are quantitative genetics and molecular biology.

• Francisco M. De La Vega, Mexico City, Mexico. Instructor.
  His BioMOO character is Francisco. E-Mail: fvega@gene.cinvestav.mx.

  Francisco M. De La Vega is Assistant Professor at the Department of genetics and Molecular Biology of the Center for Research and Advanced Studies of the National Politechnic Institute (CINVESTAV-I.P.N.) located at Mexico City, where he teaches a course on Computer Applications to Molecular Biology each year. He is interested in searching sequence patterns that might be related to gene expressivity using statistical, graphic and artificial intelligence methods. He is particularly interested in the role of preferential codon usage of lambodid bacteriophage genes in modulating viral gene expression during infection.

• Dave Wheeler, Baylor College of Medicine, Texas, USA.
  His GNA-Lab character is DaveW. Email:wheeler@heron.mbcr.bcm.tmc.edu.

  Prof. Dave Wheeler PhD is Director of the Molecular Biology Computational Resource (MBCR), the Medical Informatics Education Center (MIEC), and the Learning Resource Center (LRC) at Baylor College of Medicine. He teaches the theory and practice of sequence analysis.

Summer 1996 VSNS-BCD Consultants and Consulting Students.

• Christopher P. van Buskirk, Biomedical Supercomputing Center-Ntl Cancer Inst, USA. Java Consultant.
  His BioMOO character is VBuskirk. Email: vbuskirk@ncifcrf.gov.

  Chris van Buskirk is a senior systems administrator at The Frederick Biomedical Supercomputing Center, the world's only supercomputing facility devoted entirely to biomedical research. His interests involve the application of computational methods to problems such as protein folding, rational drug design, neural motor control and classification through self-organization.

• David T. Croke, Royal College of Surgeons, Dublin, Ireland. Proof-reader.
  His BioMOO character is Marvin. E-mail: dtcroke@rcsi.ie.

  David Croke teaches genetics at the Royal College of Surgeons in Ireland (Dublin). He works on the molecular genetics of inherited metabolic disease, especially galactosaemia and phenylketonuria.

• Scott Delinger, Edmonton, Alberta, Canada. Consulting student on HTML verification.
  His BioMOO character is SDelinger. Email: Scott.Delinger@ualberta.ca.

  Dr. Scott Delinger is a research associate in Prof. Norm Dovichi's research group in the Department of Chemistry, University of Alberta. He is writing and evaluating basecalling software for DNA sequencing in gel-filled capillaries. When not working with computers, he's playing on them (Mac PowerBook 5300cs, PowerMac 7100/80, Sparc5 (Solaris 2.4), and a 486DX4/100 (Linux 1.2.13)).

• Christian Frosch, University of Mainz, Germany. WWW-Surfer.
  His Biomoo character is: ChristianF. Email: frosc000@mzdmza.zdv.uni-mainz.de.

  Christian Frosch is a PhD student at the university of Mainz, Germany. He is working in the field of glycobiology and interested in the analysis of structure and function of N- and O-glycans.

• Kurt Giles, Weizmann Institute of Science, Israel. Glossary Curator.
  His BioMOO charcter is Kurt. Email: kurt@sgjs4.weizmann.ac.il.

  Kurt Giles is a post-doc at the Weizmann Institute of Science, Israel. His main reserch interests is the structure and function of proteins involved in neurotransmission and their relationship to neurodegenerative diseases.

• Lewis J. Gramer, Lattice Trading, Boston, Massachusetts, USA. Perl code reviewer.
  His BioMOO character is Lew. Email: dedalus@latrade.com

  Lew Gramer is Senior Engineer at Lattice Trading, where he develops object-oriented real-time equity trading applications and portfolio optimization and analysis systems for the money management industry. Lew's professional interests include graphical data representation, mathematical computing, statistical analysis, finance, and object-oriented design. He hopes to one day make a professional technical contribution to the mapping and interpretation of the human genome.

• Alessandro Guffanti, Telethon Institute of Genetics and Medicine, Milano, Italy. Helped a lot with Chapter 1.3.
  His BioMOO character is Gufo. Email: guffanti@tigem.it

  Alessandro Guffanti is a junior research fellow at TIGEM , a research center focused on the mapping, cloning and characterization of genes involved in human genetic diseases. His primary role is helping the scientists in coping with informatics in general and bioinformatics in particular. Part of this service activity is the development of specific training courses and the implementation of useful tools and programs through an intuitive interface.

• Peter Hjelmstrom, Karolinska Institute, Stockholm, Sweden. Guinea Pig Group.
  His BioMOO character is HLA. E-mail: Peter.Hjelmstrom@medks.ki.se

  Peter Hjelmstrom is an MD/PhD student currently interested in the molecular genetics of the autoimmune disease myasthenia gravis. He is doing laborations both in vivo, in vitro and in silico.

• Sophia Kossida, Oxford University, UK. BioMOO Consultant.
  Her BioMOO name is SophiaK. E-mail: sophia.kossida@merton.ox.ac.uk

  Sophia Kossida is a first year PhD student, carrying out research in molecular evolution/phylogenetics and epidemiology, being a member of the evolution group. She is doing a modelling project as well on drug design.

• Michael Lappe, University of Paderborn, Germany. Art Director.
  His BioMOO charcter is LAPPE. E-mail: lst@uni-paderborn.de

  Michael Lappe is a MSc student at the Department of Mathematics and Computer Science, University of Paderborn, writing his thesis in the field of multiple alignment algorithms. Further interests are in the simulation and visualisation of biochemical interactions, algorithmic learning and structure prediction.

• Feng Qian, University of Chicago, U.S.A. Help Guide - Mac Platform.
  His BioMOO character is Feng. E-mail:fqian@midway.uchicago.edu

  Feng Qian is a PhD student at Dept. of Pharmacological & Physiological Sciences, The University of Chicago, ILLINOIS, U.S.A. He is working on ion channels and has a strong interest in computers.

• Martin Renner, University of Otago, Dunedin, New Zealand. Consulting student.
  His BioMOO name is MartinR. Email: martin.renner@stonebow.otago.ac.nz

  Martin Renner is a MSc student working on on evolutionary ecology of Little Blue Penguins. He also has a strong interest in the potentials and limitations of molecular systematics.

• Richard J. Resnick, Apple Pi, Ashland, Massachusetts (USA). Perl Consultant.
  His BioMOO character is rjr. Email: rjr@applepi.com.

  Richard Resnick is Director and Chief Engineer of Apple Pi, a consulting firm focusing in BioInformatics and other areas of computation. His current projects include the development of a new revision of Primers! for the Mac, as well as many consulting projects with Biotech firms in the Boston area.

• Paolo Romano, National Institute for Cancer Research and Advanced Biotechnology Center, Genova, Italy. Mirror site curator.
  Email:paolo@risc1.ist.unige.it

  Paolo Romano is a Research Assistant at the Biotechnology Department of the National Institute for Cancer Research of Genoa. He is in charge of technical issues of the Biotechnology Information Services group, that was set up with the aim of creating databanks on availability of biological materials (such as cell lines and synthetic oligonucleotides) within European collections (Interlab Project), They are currently distributed by means of WAIS/Gopher/WWW servers.

• Hershel Safer, Waltham, Massachusetts, USA. Unix Consultant / Guinea Pig Group.
  His BioMoo character is Hersh. Email: h.safer@ieee.org, hersh@cric.com.

  Dr. Hershel Safer is a manager of scientific programming in the bioinformatics group at Genome Therapeutics Corp. He is interested in issues in large-scale fragment assembly and in general DNA and protein sequence analysis.

• Andrea Schafferhans, Technical University Darmstadt, Germany. Guinea Pig Group.
  Her BioMOO name is AndreaSch. Email: dh74@hrzpub.th-darmstadt.de.

  Andrea Schafferhans is a biochemistry student (8th semester) at the Technical University in Darmstadt, Germany. She is interested in prediction of Protein (Secondary) Structure and Molecular Modelling.

• Joelle Thonnard, Catholic University of Louvain, Belgium. Help-Guide - PC-platform.
  Her BioMOO name is JoelleT. E-mail: thonnard@lbcm.ucl.ac.be

  Joelle Thonnard is an MD/post-graduate student in clinical biology. She is working on HLA-typing and also, as a molecular biologist consultant, on vancomycin resistant enterococci. She is training herself in computer-applied molecular biology, mainly sequence comparison.

• Chee M VUN, Prince of Wales Hospital, Haematology Department, Sydney, Australia. Help-Guide - PC-platform.
  His BioMOO character is CheeMV. E-mail : cm.vun@unsw.edu.au

  Chee M VUN is a haematologist currently researching on the interaction between the heparin-dependent antibody and heparin-platelet factor 4 complex. He is interested in computer modeling of protein-protein and protein-carbohydrate interactions.

• Some consultants never submitted a self-description. Please take a look at the Summer 1996 Closing Address, which lists all consultants.

Summer 1995 VSNS-BCD Consultants and Consulting Students.

• Note that some entries may be outdated. Also, some consultants never submitted a self-description. Please take a look at the Summer 1995 Closing Address, which lists all consultants.

• Nikolaj Blom, Technical University of Denmark, Copenhagen, Denmark. Biblioglossarist?.
  His BioMoo character is NikoB. Email:nikob@cbs.dtu.dk.

  Nikolaj Blom has a Master's degree in biochemistry and molecular biology and is now a PhD-student at the Center for Biological Sequence Analysis. He is studying the processing of viral proteins using information theory and neural networks.

• Paul Brennan, Trinity College, Dublin 2, Ireland. Consulting Student helping with BioMOO programming.
  His BioMOO character is PaulB. E-mail:brennanp@otto.tcd.ie.

  Paul Brennan is a PhD student at Trinity College, Dublin. He is primarily a wet scientist working on the transcription factor NFkappaB but has a stong interest in computers.

• Mandy R Caird, University of Colorado, Denver. Consultant and Art Director.
  Her BioMOO/GNA character is Mandy, Email:cairdm@essex.hsc.colorado.edu.

  Mandy R Caird is a Post Doctoral Fellow at the University of Colorado, Denver, Colorado, where she works in the Neurology Department on Multiple Sclerosis.

• Chad Childers, Ford Motor Company, Dearborn, MI, USA. Plenary discussions.
  Email: chad@quality.ta.ford.com

  Chad is in charge of a software project at Ford, and would be glad of offers to assist him with translation of his User Guide into German! His undergraduate degree is in Cellular and Molecular Biology, and his research interests are developmental genetics and biocomputing. He would also like to hear about biocomputing job openings, especially those that have an associated Ph.D. program.

• Christian Kiesewetter, Bielefeld, Germany. Consulting student concerned with technical matters about HTML-documents and mailing-lists.
  His BioMOO character is ChrisK. Email: ickiesew@techfak.uni-bielefeld.de.

  Chris Kiesewetter is a fourth year student of computer science at the University of Bielefeld. He is interested in Practical Informatics and is trying to train himself in biocomputing.

• Sophia Kossida,Trinity College,Dublin 2,Ireland. Consulting student: "Guinea Pig".
  Her BioMOO character is SophiaK. E-mail: skossida@otto.tcd.ie.
  (See also the the updated entry, in the list of ``Summer 1996 VSNS-BCD Consultants and Consulting Students''.)

  Sophia Kossida is a PhD student at Trinity College, Dublin. She is interested in the general area of Molecular evolution, and she is currently working on a project: Gene Duplication and Chromosomal Evolution in the Yeast Saccharomyces cerevisiae.

• Jeff Kreher, Universitaet Stuttgart, Germany. Consulting student concerned with organizing on-line plenary discussions at BioMOO.
  His BioMOO character is 'jeffery_b'.Email: zc431122@rpool1.rus.uni-stuttgart.de.

  Jeff Kreher is currently studying abroad for one year before returning to the states for medical school. Studying Biochemistry but interests cover every aspect of academia. Especially interested in medical applications of growing computer technology and information.

• Mykol Larvie, Boston, Massachusetts, USA. Consulting student for self-assessment forms.
  His BioMOO character is mykol. Email:mykol@mit.edu.

  Mykol Larvie is an MD/PhD student attending Harvard Medical School in his 2nd year of graduate school. He is studying signal transduction proteins generally and in particular is working to obtain crystal structures of intracellular domains of cell-surface receptors.

• Chris Lilley, MAN-T&EC, University of Manchester, UK. Consulting Student helping with registration, Web (CGI, HTTP, HTML) issues, document portability and graphics interchange.
  His BioMOO character is ChrisL. Email:chris.lilley@mcc.ac.uk

  Chris Lilley is a training development officer at MAN-T&EC and a member of the Computer Graphics Unit at the University of Manchester. He has written training materials on various aspects of Computer Graphics, Scientific Visualisation ( introductory and advanced courses). He is currently writing two courses on Internet Skills for Bioinformatics. Chris is brushing up his rusty Biology skills.

• Mark Pallen, Imperial College, London, England. Glossary curator and student.
  His BioMoo character is MarkP. Email: m.pallen@ic.ac.uk.

  Mark Pallen is a medically qualified microbiologist, currently studying for a PhD on a Wellcome Truct Research Leave Fellowship at Imperial College. His current research project is aimed at investigating the links between stationary phase genes and pathogenicity in S. typhimurium. He also runs the Microbial Underground, with its On-Line Course in Medical Bacteriology.

• David G. Pisano, Universidad de Oviedo, Asturias, Spain. Technical and Administrative Advisor.
  His BioMOO character is DavidGP. Email:dgpisano@biosun.quimica.uniovi.es.

  David G. Pisano is a Graduate Molecular Biology student at the Universidad de Oviedo, Asturias, Spain. He is training himself in computer-applied molecular biology.

• Gerard Pujadas, Universitat Rovira i Virgili, Tarragona, Catalonia. He is our external resource manager.
  His BioMOO character is GerardP. Email:invbq1@quimica.urv.es.

  Gerard Pujadas is a PhD student at the Universitat Rovira i Virgili in Tarragona (Catalonia). He is doing his PhD in the "novo design" of tim-barrel like proteins. He is very interested in the use of computers to molecular biology and the use of Internet resources for protein analysis.

• Paolo Romano, National Institute for Cancer Research and Advanced Biotechnology Center, Genova, Italy. Mirror site curator.
  Email:paolo@risc1.ist.unige.it

  Paolo Romano is a Research Assistant at the Biotechnology Department of the National Institute for Cancer Research of Genoa. He is in charge of technical issues of the Biotechnology Information Services group, that was set up with the aim of creating databanks on availability of biological materials (such as cell lines and synthetic oligonucleotides) within European collections (Interlab Project), They are currently distributed by means of WAIS/Gopher/WWW servers.

• Dierk Seeburg, Tempe, USA. BioMOO Help-Guide.
  His BioMOO character is Dierk. Email: dierk.seeburg@asu.edu.

  Dierk Seeburg is a third year Ph.D. student in the Department of Botany at Arizona State University. His main research area is the molecular biology of photosynthesis, in particular mutational and structural aspects of photosystem II in the cyanobacterium _Synechocystis sp._ PCC 6803. He is affiliated with the Center of Early Events in Photosynthesis at Arizona State University.

• Toru YAO, Senior Scientific Advisor, Yokohama Research Center, Mitsubishi Chemical Corporation, JAPAN.
  E-mail; yao@rc.m-kasei.co.jp. [I've lost contact; if you can help, please send email to fuellen@dali.Mathematik.Uni-Bielefeld.DE]

  Toru YAO has beeen involved in the Protein Engineering Research for these ten years as a research director. He is especially interested in the computer applications for various aspects of protein analysis including protein sequence analysis, structural database(PDB) analysis, structure prediction, structure determination(X-ray,NMA), protein design and modeling. The next problems would be how to analyze the interactions between proteins and other biomolecules.

• Michal Wittner. Consulting student, GeorgF's "Guinea Pig".
  His BioMOO character is Michal. Email: wittner@lf1.cuni.cz.

  Michal Wittner teaches human physiology at the Charles University, Prague. He currently works on immediate early genes expression in gerbil transient forebrain ischemia at the University of Kuopio.

Back to Biocomputing Course Home Page.
VSNS-BCD Copyright 1995, 1996.
Georg Fuellen