User:59.161.72.124/Java Bioinformatics Programmers

Some notable Bioinformatics Java Programmers:

Richard Holland

His career in bioinformatics started at AgResearch in New Zealand, then moving to the Genome Institute of Singapore. He used BioJava for a while but got seriously involved after working with Mark Schreiber on the DengueInfo project in Singapore, which required BioJava to be able to work seamlessly with BioSQL databases. As this was not completely possible in version 1.4, they produced the BioJavaX extensions released in version 1.5 that allow BioJava to use the Hibernate framework for accessing BioSQL. He spent the next couple of years after Singapore working at the EBI at Hinxton on the BioMart team. In Summer 2007 he mentored a student for the Google Summer of Code, Boh-Yun Lee, who worked on some phyloinformatics modules for us. The GSoC'07 project was organised by NESCent. He is now self-employed as part of a new biotech startup in Cambridge, Eagle Genomics, and in his spare time am working on BioJava 3.

Andreas Prlic

Andreas Prlic is Senior Scientist at the RCSB-PDB database in San Diego, California. Prior to this he worked as a PostDoc at the Wellcome Trust Sanger Institute, Cambridge, U.K. Currently he is acting as project leader for BioJava. He developed the protein structure API. Other projects he was working on include e.g. SPICE a browser for protein sequence and structure annotations, based on the Distributed Annotation System.

Thomas Down

Thomas is a co-founder of Biojava. He has four years of bioinformatics experience, with particular interests in machine learning and data distribution architecture. He as written a book on Linux installation, and wrote a regular magazine column of programming tips. Thomas has recently completed a PhD in bioinformatics at the Wellcome Trust Sanger Institute. His research focuses on the application of machine learning techniques to the identification of important biological signals, and has developed a transcription start site predictor which outperforms all other techniques.

Matthew Pocock

Matthew is a co-founder of Biojava, and has developed (with Thomas Down) much of the Biojava library. He has completed a PhD in bioinformatics at the Wellcome Trust Sanger Institute/ Cambridge University. His PhD centered on the problems faced when analysing data-sets generated from genomic research. Existing methods did not scale gracefully with the vast quantity of information. He developed ways of analysing these very large data sets and also software capable of representing genomic data efficiently. Matthew is now at the University of Newcastle Upon Tyne, investigating ways that existing scalable solutions, such as Biojava, can be leveraged through web service and grid technologies for life sciences.

Keith James

Keith became involved in biojava while working at the Sanger Institute.Keith has made many important contributions to biojava including introducing the ant build script and JUnit tests. He also did important work with the early OBDA architecture and the SSBind packages and BLAST/ FASTA parsers.

David Huen

David left a career in petroleum refining in 1986 to do an MSc followed by a PhD in molecular biology. He worked initially on cancer biology and cell signalling but has since switched to Drosophila genetics. He is currently a postdoc with the Ashburner group doing both bench work and bioinformatics. David initially learnt BioJava when he had to move large numbers of annotations he accumulated on certain regions of the Drosophila genome when the coordinate framework of the Drosophila genome was changed in a new release. That task remains most cussedly undone but he has moved on to using BioJava routinely in other activities. His most lasting contributions to BioJava tend to be bugfixes but his most recent contribution was a SymbolList regex package. On the other hand, some of his earlier contributions will most deservedly be taken out back and shot.His current BioJava activity centres around HMM models for comparative genomics and novel software approaches for analysis of chromatin immunoprecipitation microarray results. Most of this software will eventually end up in BioJava somewhere.

Mark Schreiber

He first became involved with BioJava in 2000. He was doing his PhD in New Zealand and He needed a Java package that could produce HMMs suitable for gene finding algorithms. BioJava had just arrived and did what he needed it to do. During this time he added some support for circular genome sequences and locations, much of the DistributionTools class, tools to read Phred data and improved the serialization of the core BioJava objects. Some of these contributions have been more succesful than others. He also used BioJava in his PhD research to calculate the information content of motifs and display these graphically.In 2001 he joined AgResearch, an NZ based agricultural biotech company, as a Bioinformatics Consultant. There he used BioJava to detect SNPs and micro-satellites in EST contigs. While at AgResearch in 2003 he began work on the Biojava in Anger cookbook which he still try to keep up to date when he have time.In 2004 he moved to Singapore to work as a Principal Scientist with the Novartis Institute for Tropical Diseases. there he use BioJava to support the Tuberculosis and Dengue Fever drug discovery programs. His research interests have expanded to include evolution, phylogeny and molecular and structural modelling. Some of these may find there way into BioJava soon. He is also working with Richard Holland from GIS using biojava and biosql to make a dengue virus sequence database called dengueinfo. The are also working on an experimental extension and hopefully backwards compatable upgrade to biojava called biojavax (watch this space).He is sporadically helping to write a book on BioJava with a projected completion date that is very fuzzy just now. His current thinking is that he will make it a Wiki manual or a DocBook xml in CVS so everyone can edit it.

Michael Heuer

Michael Heuer has been a Biojava contributor since 2000.

Phillip Lord

He is a lecturer at the School of Computing Science at Newcastle since Sept, 2005. He teach mostly on the MSc Bioinformatics and Computational Biology, which is run from Computing Science, but taught by quite a few schools (five at the last count!) from within the University. His research covers a variety of different areas; mostly it focuses on the use of ontological technology in biology, or more generally mechanisms for presenting and publishing scientific information. He also developed the idea of the Knowledge Blog which has been supported by Ontogenesis Network, and has resulted in the start of a Ontology Encyclopedia. Part of this work recently appeared on the Guardian science blogs.Previously, He has worked on a wide variety of projects, including ONDEX which is a data integration framework for systems biology, and the CARMEN project, which is providing support for the sharing and resuse of neurosciences data and early projects such as myGrid and ComparaGRID.

Christoph Steinbeck

His research interests have involved the elucidation of chemical structures of metabolites. He has was one of the first chemists to develop open source tools for cheminformatics. He initiated JChemPaint and was founder of the Chemistry Development Kit. Currently he heads the Cheminformatics and Metabolomics group at the European Bioinformatics Institute in the United Kingdom. Together with a few other chemists he was a founder member of the Blue Obelisk movement in 2005.

Egon Willighagen

Postdoctoral researcher at the Department of Bioinformatics - BiGCaT at Maastricht University. I study the role of machine representation of knowledge and hypothesis in life sciences, drug discovery, and toxicology, involving chemometrics and semantic web technologies. In the past, I have applied research on this in QSAR, crystallography and metabolomics. Open source programming is my main hobby resulting in participation in, amongst many others, MetWare, Bioclipse , Chemistry Development Kit , Jmol , and Oscar.

Subrata Sinha

He is an Assistant Professor in Centre for Bioinformatics Studies,Dibrugarh University. He enetered into Bioinformatics Programming in 2006. He has developed a Java open source libraries for medical sciences.

Dr. Tancred Frickey,Applied Bioinformatics,Universitaet Konstanz developed many Bioinformatics Softwares like JTreeView,CLANS etc.

Professor Gezelter

Professor Gezelter received his BS in Chemistry and Philosophy from Duke University. He then spent a year at the University of Cambridge as a Churchill Scholar. He obtained his Ph.D. from the University of California at Berkeley for research on quantum effects in unimolecular reaction dynamics. During his postdoctoral studies at Columbia University, he developed computational methods and theories to understand diffusion in liquids and glassy materials. Professor Gezelter was a recipient of the Camille and Henry Dreyfus New Faculty Award for 1999 and was awarded the National Science Foundation's Faculty Early Career Development (CAREER) Award in 2002.

 Münz M and Biggin PC

Professors of Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom has Deveoped JGromacs A Java library designed to facilitate the development of cross-platform analysis applications for Molecular Dynamics (MD) simulations.

Volker Hähnke, Andreas Schüller and  Prof. Dr. Gisbert Schneider

SmiLib v2.0 was developed by Volker Hähnke during an internship under supervision of PhD student Andreas Schüller and Prof. Dr. Gisbert Schneider at the Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.

David Kofke and Andrew Schultz of Department of Chemical and Biological Engineering at University at Buffalo has developed Etomica a Java API and development environment for construction and implementation of molecular simulations. The API is a set of classes that can be employed to construct a molecular simulation in Java. Simulations may be constructed with them by programming in Java with a text editor, or by using the Etomica development environment. The development environment provides a graphical interface for constructing, running, and saving simulations based on the API. The Etomica environment provides for dynamic modification and interrogation of the simulation, while it is in progress.

Stephen Ramsey

Stephen Ramsey in the laboratory of Hamid Bolouri at ISB wrote ISBJava. The ISBJava project is a library (collection) of classes written in the Java programming language, that are intended to be used for research in computational biology.

Michael Hucka and His Team

Michael Hucka (Ph.D. in Computer Science and Engineering) is a Member of the Professional Staff at Caltech. He has Chaired the SBML Editors and SBML Team since 2003. He works on all aspects of SBML. SBML is the result of many people's efforts over many years.