Jalview has been developed in Geoff Barton’s group since 1995. Jalview Version 1 was developed at The University of Oxford and EMBL-EBI. Since 2001, Jalview has been developed in Geoff Barton’s Group at the University of Dundee, and [Version 2] was launched in 2005.
The current members of the Jalview core team are:
- James (Jim) Procter (Jalview Coordinator)
- Ben Soares (Research Software Engineer)
- Mateusz Warowny (Research Software Engineer)
- Suzanne Duce (Training and Outreach - joint with Dundee Resource for Protein Sequence Analysis and Structure Prediction)
The team works closely with the Dundee Resource for Protein Sequence Analysis and Structure Prediction, which provides many of Jalview’s web services. Jalview also incorporates many community contributions. You can see the full list of contributors and past members at the bottom of this page.
Jalview’s core team work closely with the following collaborators:
Jalview’s core team at Dundee is currently supported by the following grant:
- 2020-2024 Wellcome Trust: 218259Z/19/Z The Jalview resource for biological sequence, structure and function analysis: 2019 and beyond.
Completed grants from the UK’s BBSRC (Biotechnology and Biological Sciences Research Council) and the Wellcome Trust
- 2014-2019 BBSRC: BB/L020742/1 The Jalview Resource for Sequence Analysis and Annotation.
- 2013-2018 Wellcome Trust: 101651/Z/13/Z Extending The Jalview Resource for Biological Sequence Alignment and Analysis
- 2009-2014 BBSRC: BB/G022682/1The Jalview Resource for Sequence Analysis and Annotation - www.jalview.org.
- 2004-2007 BBSRC: BBS/B/16542 Visualisation of Biological Sequences, Alignments and Structures - VAMSAS.
The Jalview resource also relies on support from the Dundee Resource for Sequence Analysis and Protein Structure Prediction which is supported by the following grant:
- 2013-2018 BBSRC: BB/J019364/1 The Dundee Resource for Protein Structure Prediction and Sequence Analysis.
Jalview’s primary authors and contributors are listed below. The ‘AUTHORS’ file in Jalview’s source provides the most up to date list of contributors for each release. Scroll down further for details of specific features implemented through community contributions and open-source supported student projects.
- James (Jim) Procter
- Mungo Carstairs
- Ben Soares
- Kira Mourao
- Tochukwu Ofoegbu
- Jan Engelhardt
- Lauren Lui
- Anne Menard
- Natasha Sherstnev
- Daniel Barton
- David Roldan-Martinez
- Yann Ponty
- Andrew Waterhouse (Joint first author Jalview 2)
- Michele Clamp (Creator of Jalview 1)
- James Cuff (Jalview 1)
- Steve Searle (Jalview 1)
- David Martin (coinvestigator for original Jalview 2)
- Geoff Barton (Chief Bugtester for all versions of Jalview)
We would like to specifically thank the following people who have contributed code, or otherwise collaborated with the core Jalview team, in roughly reverse historical order:
- Bob Hanson (St. Olaf College, USA) created SwingJS and helped us adapt Jalview’s source code to create JalviewJS
- Thomas van Aalten (Astrophysics program, St. Andrews) - worked as a summer student in 2017 and 2019 to add support for working with the HMMER command line tools from Jalview and visualising sequence profiles.
- Mateusz Warowny (Physics Masters, U. Dundee) created Slivka - which provides Jalview’s third-generation of web services (released in 2020).
- Paolo di Tomasso (Center for Genomic Regulation, Spain) Added support for parsing T-COFFEE score files and displaying them on the alignment, introduced in version 2.8.
- David Roldan-Martinez internationalised (i18n) Jalview’s user interface and crowdsourced the first version of Jalview’s spanish UI.
- Daniel Barton (Physics Masters, U. Dundee) added the RNAAliFold client and JABAWS service whilst a summer scholar with the Jalview team in 2013.
- Jan Engelhart (Stadler Bioinformatics Group, University of Leipzig, Germany) Jan was our second Google Summer of Code student, in 2011, and implemented the RNA structure consensus logo, and embedded VARNA in the Jalview v2.8 desktop.
- Lauren Lui (Lowe Lab, University of California at Santa Cruz, USA). Lauren was our first Google Summer of Code student in 2010, and implemented the RNA secondary structure annotation, and RNA helix colour scheme introduced in version 2.8.
- Bernd Brandt (originally in Jaap Heringa’s group at the Free University of Amsterdam, last seen at the Academic Centre for Dentistry. Amsterdam (ACTA)). Bernd helped develop the Multi-Harmony protein alignment analysis web service.
- Benjamin Schuster-Böckler (originally at Wellcome Trust Sanger Institute, last seen at University of Oxford) Benjamin contributed the Stockholm parser introduced in version 2.1.
- Andreas Prlic (whilst at Wellcome Trust Sanger Institute, then the San Diego Supercomputing Center, USA). Andreas wrote the first Java DAS client library, dasobert, used in Jalview 2.1 through to version 2.7, and made many suggestions on how Jalview could better use DAS.
If we’ve forgotten you, or you’d like to update your details, please contact us!
- The original Jalview 2 logo and site design was created by Andrew Waterhouse in 2005.
- The Jalview logotype was created in 2012 by Barry Strachan.
- The logo for Jalview Develop was adapted from the Jalview logotype in 2020 by Ben Soares with changes inspired by the Penrose Triangle. It shows a more fluid representation of the logo to indicate the more fluid nature of new features in Jalview Develop. Read into the “impossible twist” what you will!
- The logo for Jalview Test was adapted from the Jalview logotype in 2021 by the Jalview Team. The alteration of the middle square to a white square stylises a checkbox representing the final stages of checking before the next release.
- The logo for JalviewJS was adapted from the Jalview logotype in 2022 by the Jalview Team. The square-based logotype has the ‘JS’ from the commonly used square-based Javascipt logos added in black. To ensure contrast of the black letters on all backgrounds whilst not covering up the Jalview logo in lower resolution, the letters are outlined in a continuation of the logo colouring.
Jalview Web Site Design
The current Jalview website is developed in Hugo . It was created by Adrian Simmons who modernised the site and migrated it from Drupal to Hugo in early 2021. It was put into production in August 2022.
The Jalview website makes use of open source projects:
- Font Awesome for icons
- clipboard.js for copy-to-clipboard functionality
- video.js for inline videos
- Lightbox2 for image display
- Osano open source cookie consent banner for cookie consent
- Lightbox by jhvanderschee for overlaid YouTube videos.
The Drupal Site design and development was done by Ryan McLaughlan and Andrew Millar in the Web Services group at the University of Dundee College of Life Sciences 2010. Older Jalview sites were developed in Dreamweaver, or Plain Old HTML.
Jalview Version 1
Jalview was first developed from 1995-1997 at The University of Oxford and then EMBL-EBI from 1997-2001. Since 2001 the core development team has been based in the School of Life Sciences at The University of Dundee.
- Michele Clamp
- James Cuff
- Stephen Searle
- Geoff Barton