User:Kehan Harman
My Blog I am currently a researcher at the Natural History Museum, London working on part of the Scratchpads Project specifically focusing on development of the GBIF Vocabularies Service and other GBIF sponsored Scratchpads.
My background is a mixture of Botany/Biology with some work both in traditional morphological systematics as well as population genetics / molecular ecology work. Most of my experience with descriptive data comes from helping to maintain and develop GrassBase - The Online World Grass Flora at the Royal Botanic Gardens, Kew.
Contents
Summary
Web Application Developer in a variety of biodiversity informatics applications. Particularly interested in data transformations and social interaction using generic open source tools. I combine strong background in traditional alpha taxonomy and modern molecular techniques with a good understanding of the current state of the art in biodiversity informatics and familiarity with a whole suite of software tools and programming languages.
Contact Details
| Name | Kehan Tristam Harman |
| Born | 16 May 1977, Mbabane, Swaziland, Africa |
| Address | 63 Balvernie Grove, Southfields, United Kingdom |
| Tel | +44 (0)20 8785 4386 (home) +44 (0)78 5938 4584 (mobile) |
| kehanharman@gmail.com | |
| Web | http://kehan.wordpress.com http://www.linkedin.com/in/kehan |
Qualifcations
| M.Sc. | in Bioinformatics (77%). 2005-2007. Modules including Perl & Java Programming, Bioinformatics Algorithms & Tools, Statistics, Database Management (MySQL & Oracle). Group project in software engineering. Research project: GrassBase - Steps toward integrating the Online World Grass Flora. Involved developing a prototype Drupal based Grass portal for integration of Kew's institutional grass databases. Cranfield University, UK. |
| B.Sc.Hons | in Botany (73%). 2000: Options: Advanced Systematics, African Phytogeography, Molecular Ecology and Climate Change. Rhodes University, Grahamstown, South Africa. |
| B.Sc. | in Botany (77.5%) and Microbiology (70.5%). 1997-1999: Rhodes University, Grahamstown, South Africa. |
| I.B. | International Baccalaureate Diploma. 1994-1995: Higher Level: Biology (6), Chemistry(5) and Mathematics (5); Subsidiary Level: English Literature (4), French (5) and Geography (5). Waterford Kamhlaba, United World College of Southern Africa, Mbabane, Swaziland. |
| O-Level | University of Cambridge O Level Certificate. 1992-1993: Nine O-Levels with an aggregate 13 Points. Waterford Kamhlaba, United World College of Southern Africa, Mbabane, Swaziland |
Publications
Smith, VS, Rycroft, SD, Harman, KT, Scott, B, Roberts, DMcL. In Press. Scratchpads: a data-publishing framework to build, share and manage information on the diversity of life. BMC Bioinformatics.
Roberts, DMcL, Rycroft, SD, Brake, I, Harman, KT, Scott, B, Smith, VS. 2008. Getting Taxonomy onto the Web. The Systematist[1]30: 3.
Mayo, SJ, Allkin, R, Baker, W, Blagoderov, V, Brake, I, Clark, B, Govaerts, R, Godfray, C, Haigh, A, Hand, R, Harman, K, Jackson, M, Kilian, N, Kirkup, DW, Kitching, I, Knapp, S, Lewis, GP, Malcolm, P, von Raab-Straube, E, Roberts, DM, Scoble, M, Simpson, DA, Smith, C, Smith, VS, Villalba, S, Walley, L, Wilkin, P. (2008) Alpha e-taxonomy: responses from the systematics community to the biodiversity crisis Kew Bulletin[2]63:1-16. DOI: 10.1007/s12225-008-9014-1
Paton, AJ, Brummitt, N, Govaerts, R, Harman, K, Hinchcliffe, S, Allkin, R, Nic Lughadha, E. (2008) Towards Target 1 of the Global Strategy for Plant Conservation: a working list of all known plant species—progress and prospects Taxon[3]57(2):602-611.
Harman, KT, Clayton, WD. (2007) Recent developments in Kew's grass databases (GrassBase) Kew Bulletin 62: 375-379. Clayton, W.D., Harman, K.T. & Williamson, H. (2006 onwards) World Grass Species: Descriptions, Identification, and Information Retrieval. Published online: World Grass Species: Descriptions, Identification, and Information Retrieval Clayton, WD, Harman, KT, Williamson, H. (2006 onwards) World Grass Species: Synonymy. Published online: World Grass Species: Synonymy.Wilkins, KJ, Harman, KT & Villet, MH. (2006) Recruitment behaviour in the ponerine ant, Plectroctena mandibularis F. Smith (Hymenoptera: Formicidae). African Entomology 14(2): 367-372.Barker, NP, Harman, KT, Ripley, BS, Bond, J. (2002) The genetic diversity of Scaevola plumieri (Goodeniaceae), an indigenous dune coloniser, as revealed by Inter Simple Sequence Repeat (ISSR) Fingerprinting. South African Journal of Botany[4]68:532-541.
Experience
Researcher – GBIF Funded, Natural History Museum, London. Mar 2008 – Present: Software development to support the GBIF ECAT programme. Using the Scratchpads (http://scratchpads.eu) framework (based on Drupal) to develop various community interaction tools including the GBIF vocabularies and extension server (http://vocabularies.gbif.org). This involves using my taxonomic and computing background to develop a suite of Drupal modules.
Database and Collections Officer, Royal Botanic Gardens, Kew. Feb 2005 – Jan 2008: Managing and developing Kew's grass synonymy and DELTA descriptive databases, and helping to make them web accessible (see bioinformatics skills below). Curation and identification of grass and other Monocot specimens in this global collection. Included developing a prototype web portal for my M.Sc. research project (see above). Standardising nomenclature database according to TDWG content standards.
Global Checklist Project Officer – Royal Botanic Gardens, Kew. May 2004 - Jan 2005: Digitisation of herbarium specimens, help with preparation of preliminary conservation assessments and data analysis and help during preparation of final report for the iPlants (http://iplants.org) pilot project.
Office Manager & New Media Consultant – Firoco Chartered Marketers, Wimbledon. Jan – May 2004: Management of customer relationship management databases for our clients, general office administration and development of marketing materials including html emails and websites including company website http://www.firoco.co.uk.
Administrator for Looked After Children Reviews – London Borough of Merton. Feb - Dec 2003. Diary management and coordination for a team of 6 independent reviewing officers. Additionally I had to process paperwork for the independent reviews within strict statutory guidelines
Volunteer – Loggerhead Turtle Conservation Project, Katelios, Kefalonia, Greece.June - Aug 2002 Assisted in monitoring the reproductive biology of Caretta caretta. Helped deliver community based conservation through public education and helped develop a project website.
IT Help-desk Assistant – Portsmouth City Council. Feb - June 2002: Desktop support for the roll-out of a new in house accounting database. Included logging calls, resetting passwords and giving remote assistance via Citrix Metaframe.
Factory Operative – First People Recruitment, Portsmouth, UK. Nov 2001 - Jan 2002: Various temporary assignments at automotive component factories.
Game Ranger – Mala Mala Games Reserve, Kruger Park, South Africa. Jan - Sep 2001: A dual role involving conservation and landscape management combined with duties included all aspects of hosting international guests at a 5 star private game reserve, including catering, bar-keeping, waitering and housekeeping as well as being solely responsible for guests needs and Guiding during meals and game drives throughout the day.
Student Researcher – Molecular Ecology Unit, Institute of Terrestrial Ecology at Furzebrook, Dorset. Dec 1999 - Jan 2000: Carrying out a research project involving the DNA fingerprinting of a South African plant population in a Molecular Ecology Laboratory.
Tutor and Demonstrator – to 1st and 2nd year Botany and Biology students - Botany Department, Rhodes University, Grahamstown, South Africa. Feb 1999 - Nov 2000: Acting as a tutor to students during practical sessions, tutorials and field excursions, including the marking of work produced.
Reference Database Management and Report Writing – Various Academic Staff, Rhodes University, South Africa. July 1998 - July 1999: Setting up and maintaining extensive databases of scientific literature, and the compilation of a number of separate research articles into a final Water Research Commission (South Africa) report.
Skills
Bioinformatics
Programming – in PHP, Perl, Java, MATLAB, and Visual Basic/VBA. PHP extensively used in Drupal module development. Visual Basic used in maintaining current grass databases including VB programs to manipulate DELTA text files and work on the user interface of the MS Access synonymy database. Java used in developing a web based reference management tool as part of a group project. Additionally some work using the AppFuse2 Java Application Development framework based on Maven, Struts and Hibernate. Perl used for text (including DNA sequence) manipulation & database connectivity.
Drupal – In depth knowledge of the Drupal open source content management framework including module development and participation in its open source development community. Knowledge of Drupal concepts including Hooks, Taxonomy, Nodes, Views and CCK.
Team based software development – using both Eclipse and NetBeans IDE, using SVN, CVS and GIT version control systems, with project management and issue tracking using Trac, Sourceforge, Google Code and Launchpad. Use of Wiki's including MediaWiki and TWiki for team collaboration.
TDWG Standards – Extensive experience of DELTA, TDWG content standards (geography and literature), knowledge of SDD, TCS, ABCD/DarwinCore including the TDWG Ontology. Knowledge of the OGC (Open Geospatial Consortium) standards and how they relate to biodiversity data.
Medical bioinformatics – Knowledge of a suite of software tools currently used. Working on various data types including output from microarray, mass spectrometry and gas chromatography experiments, the large molecular databases such as GenBank, Ensembl, Uniprot and PDB. Statistical analysis using both R and Matlab, sequence manipulation using Perl (inc. Bioperl) and Java (inc. Biojava).
Computer literacy – Touch typing (65 WPM), Word Processing, Spreadsheet, Database and Email in all versions of Windows, Mac OS X and Linux operating systems and system administration with extensive experience administrating Ubuntu Linux servers including software updates, backup regimes, Apache Web Server, mail handling and user management.
Hardware and software maintenance – computer building, networking and troubleshooting.
Scientific Skills
Molecular Biology – PCR, DNA extraction, manipulation, sequencing and fingerprinting.
Microscopy – Light, Scanning and Transmission Electron Microscopy.
Molecular Ecology and Systematics – Data analysis in these disciplines.
Grass morphology and taxonomy.
Communication
Verbal – Experience as a game ranger, salesperson and a tutor, work in various committees and presentation of seminars. Written – several publications, two Honours theses, posters presented at three international conferences, report writing and numerous essays.
Independence
Work in my current post is mostly self driven.
Work in my undergraduate and Honours projects was mostly self-driven.
People
Leadership
Being founding chairperson of a cultural society and working as an administrator has given me experience in the delegation and organisation involved in a leadership position.
Teamwork
Working as a Game Ranger involved close teamwork with my personal tracker and with other rangers over the radio in order to maximise game viewing for guests.
Achievements
Chair – Herbarium Computing Group, Royal Botanic Gardens, Kew. 2007 – 2008.
Member – Global Checklist Steering Group, Royal Botanic Gardens, Kew. 2006-2007.
Lillian Britten Prize for Botany III. 2000: Awarded to the top student in 3 year botany.
NRF (National Research Foundation) Freestanding Scholarship and Rhodes University Honours Degree Scholarship. 2000: Awarded for Botany Honours on the basis of my performance in my B.Sc. Degree.
Outstanding Service Award, Rhodes University Mountain Club. 1999: Awarded for aiding with the rescue of a fellow club member and for services in the executive committee of that club.
Academic Half Colours, Rhodes University. 1998 & 2000: Two merit awards based on academic performance in my first and final year of my B.Sc.
Interests and Hobbies
Rock-climbing, Hiking, Mountain Biking & Sailing
Plant and Wildlife Conservation
Computer building, programming and operation
References
David Remsen. ECAT Programme Officer. GBIF Secretariat, Universitetsparken, DK-2100 Copenhagen 15, Denmark. E: dremsen@gbif.org T : +4528751472
Dr David McL. Roberts. Researcher, Dept. of Zoology, Natural History Museum, Cromwell Road,
Dr David Simpson, Assistant Keeper for Monocots, Herbarium, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB. Current Manager E: d.simpson@kew.org T: +44 2083 325260
Dr Conrad Bessant, Senior Lecturer in Chemometrics & Bioinformatics, Cranfield Health, Cranfield University, Silsoe, Bedfordshire MK45 4DT. M.Sc.Supervisor & Course Coordinator E: c.bessant@cranfield.ac.uk T: +44 1525 863358
