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TDWG 2011 Programme Committee
by Chuck Miller 29 Apr '11

29 Apr '11

As announced earlier, the 2011 TDWG annual conference will be held on October 16-21, 2011 at the Astor Crowne Plaza Hotel in New Orleans, Louisiana located at the entrance to the famous Bourbon Street district. Hank Bart, Director of Tulane Museum of Natural History, is the local sponsor. The Programme Committee for the conference has now been organized. The Committee members are: Chair - Rusty Russell - Smithsonian National Museum of Natural History Cyndy Parr - Encyclopedia of Life Greg Riccardi - Florida State University, MorphBank Joel Sachs - University of Maryland Rich Pyle - Bishop Museum Kevin Richards - Landcare Research, New Zealand Hank Bart - Tulane Museum of Natural History Gail Kampmeier - Executive Committee liaison The Programme Committee will be contacting Interest Group Convenors regarding symposia and organization of the program. Information on accommodations, registration, program, abstract submission and other meeting details will soon be made available at www.tdwg.org. Chuck Miller TDWG Chair

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Position Opening: Biological Informatician
by Gail E. Kampmeier 26 Apr '11

26 Apr '11

Please consider or pass this announcement to someone who might be interested in applying for this position. Apologies for cross-posting. For further information please contact Erica Hanson, Human Resources, Illinois Natural History Survey, 217-333-6897, elhanson(a)inhs.illinois.edu. For technical questions, please contact: Dr. Andrew Miller, Search Committee Member, at amiller(a)inhs.illinois.edu. --Gail BIOLOGICAL INFORMATICIAN ILLINOIS NATURAL HISTORY SURVEY, a division of the INSTITUTE OF NATURAL RESOURCE SUSTAINABILITY UNIVERSITY OF ILLINOIS POSITION: The Illinois Natural History Survey, a division of the Institute of Natural Resource Sustainability, University of Illinois at Urbana-Champaign, is pleased to announce the position of Biological Informatician. PROJECT DESCRIPTION: Cyber-technology in the Biological Sciences presents a nearly unbounded landscape for development and implementation of extensible and sustainable solutions in dissemination of scientific research data. World-renowned scientific research at the Illinois Natural History Survey, the nation’s second oldest and largest biological survey, continues and with the application of cyber- technologies for integration and dissemination, will continue to have a major impact on society, science, and critical issues such as biodiversity and global climate change. We seek a highly motivated, innovative individual to contribute to a rapidly developing and transformative biodiversity informatics program at the Illinois Natural History Survey. The successful candidate will work with INHS scientists and IT staff to advise, develop, and implement sustainable and extensible database-driven web applications aimed at electronic dissemination of biological research results. Focal areas include biodiversity informatics (ecological and biotic community datasets), a developing extensible cybertaxonomy portal, and amalgamation and synthesis of the INHS natural history collections databases, which currently include more than 11 million objects. Half time will be devoted to informatics for collections-based research, while the other half will be devoted to the Species File program (http://software.speciesfile.org) JOB DESCRIPTION: The successful candidate will be expected to coordinate INHS-wide efforts to develop and implement computer-based solutions for mobilization, use, and sustainability of biodiversity data; collaborate with INHS scientific staff to solicit and secure external funding to support new and ongoing projects related to biodiversity informatics; recruit, train and supervise hourly programmers and undergraduate computer science interns to support funded projects; train INHS scientific staff in the use of biodiversity informatics tools and participate in bioinformatics standards development; serve as liaison between INHS scientists and the INHS webmaster, network administrator, and other INHS/INRS IT support staff. QUALIFICATIONS: This position requires a B.S. in Computer Science, Information Science, or Bio- (biodiversity) informatics. M.S. or Ph.D. degree desired. Emphasis in biological diversity informatics preferred. Individuals with a degree in a biodiversity-related field and relevant coursework and experience in scientific computing will also be considered. Experience with biological informatics support in a laboratory or organization setting is preferred. Experience with database-driven web application development with skills in database design and management, SQL, HTML, Visual Basic, CSS, CMS (e.g. Drupal), and scripting languages (e.g. JavaScript, Python, Perl, Ruby, PHP). Demonstrated ability with programming languages and web application frameworks is required. Familiarity with Web 2.0 programming technologies is highly desirable. SALARY RANGE: $68,000 to $75,000, commensurate with experience. This is a regular, academic professional, full-time, grant-supported, 9-month position/paid over 12-months (academic 9/12). Additional salary support for two summer months may be available through external funding obtained by the candidate through research grants or other funding opportunities.The estimated starting date is July 1, 2011. BENEFITS: Generous sick leave. State Universities Retirement System. Group health, dental, vision and life insurance. APPLICATION PROCESS: Applications must be received by May 27, 2011. To apply, all candidates must submit an online profile through https://jobs.illinois.edu by the close of the posting period. Qualified candidates must upload a cover letter which details qualifications noted above, curriculum vitae, working e-mail address, and the names, addresses, phone numbers, and e-mail addresses of three professional references. All requested information must be submitted for your application to be considered. Incomplete information will not be reviewed. For further information please contact Erica Hanson, Human Resources, Illinois Natural History Survey, 217-333-6897, elhanson(a)inhs.illinois.edu. For technical questions, please contact: Dr. Andrew Miller, Search Committee Member, at amiller(a)inhs.illinois.edu. The University of Illinois is an Affirmative Action/Equal Opportunity Employer. The administration, faculty, and staff embrace diversity and are committed to attracting qualified candidates who also embrace and value diversity and inclusivity.

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Job: NESCent User Interface Design and Web Application Developer
by Karen Cranston 02 Mar '11

02 Mar '11

[ Apologies for cross-posting ] The National Evolutionary Synthesis Center (NESCent) seeks a creative and enthusiastic individual to design user interfaces and web applications for scientific applications. The incumbent will work as part of a small informatics team in close collaboration with domain scientists. NESCent (http://nescent.org) is an NSF-funded center dedicated to cross-disciplinary research in evolutionary science. Our informatics team works closely with visiting and resident scientists to support their custom software and database development needs. All NESCent software products are open-source, and the Center has a number of initiatives to actively promote collaborative development of community software resources (http://informatics.nescent.org) Above all, we are enthusiastic about our work, about the mission of the Center, and about the contribution of informatics to that mission. Job description: The incumbent will design and develop user interfaces and web applications for databases and other software tools for sponsored scientists and staff. The job responsibilities include all stages of the software development process, including requirements gathering, design, implementation, release packaging and documentation, as part of a small team (typically 2-3 individuals) following project management best practices. We expect the incumbent to present their work at conferences and contribute to publications with scientific collaborators; interact regularly with visiting and resident scientists, other members of the informatics team and Center staff; and generally serve as an expert resource for Center personnel. The position provides opportunities for professional development. Most informatics staff work at our Durham NC offices, located adjacent to Duke University, but we do support a wide range of technologies for virtual communication with off-site staff and collaborators. Required Qualifications: * Demonstrated success collaborating with clients on custom software solutions * Experience with various stages of the software development cycle * Expertise in development and testing of user interface designs * Excellent communication skills, both virtual and face-to-face Preferred Qualifications: * M.S. or Ph.D. in Computer Science, Bioinformatics or related field * Demonstrated interest in science, particularly biology * Expertise in dynamic and interactive web technologies (JavaScript, CGI) * Expertise in rapid application development and respective programming technologies and languages (e.g., modern scripting languages and web-application frameworks such as Python/Django, Ruby/Ruby-on-Rails, and Perl/Catalyst). * Expertise in graphic design * Expertise in data visualization and/or scientific data integration * Expertise in software usability design and assessment * Expertise in web service (SOAP, REST, XML, JSON) and semantic web technologies * Fluency in Java programming * Prior experience in relational database programming (PostgreSQL or MySQL) * Experience with open-source, and collaborative, software development How to apply: Please send cover letter, resume and contact information for three references to Dr. Karen Cranston, Training Coordinator and Bioinformatics Project Manager (karen.cranston(a)nescent.org) Informal inquires or requests for additional information may be directed to Dr. Cranston by email or phone (+1-919-613-2275). -- ~~~~~~~~~~~~~~~~~~~~~~~ karen.cranston(a)gmail.com ~~~~~~~~~~~~~~~~~~~~~~~

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LSID and GUID Applicability Statements approved as new TDWG Standards
by Chuck Miller 21 Feb '11

21 Feb '11

The TDWG Executive Committee has approved the Life Sciences Identifiers Applicability Statement (LSID_AS) and the Globally Unique Identifiers (GUID_AS) Applicability Statement as new TDWG standards. The Executive committee acknowledges Kevin Richards of Landcare New Zealand as author of the GUID Applicability Statement. Likewise, Kevin Richards, Ricardo Pereira (TDWG Infrastructure Project), Donald Hobern (Atlas of Living Australia), Roger Hyam (TDWG Infrastructure Project), Lee Belbin (TDWG Infrastructure Project) and Stan Blum (California Academy of Sciences) as co-authors of the LSID Applicability Statement. The committee also greatly appreciated the patience and perseverance of Ben Richardson of the Department of Environment and Conservation of Western Australia who was the Review Manager for these standards. The process, as can be seen from the institutional associations, was in this case longer than all would have liked, but we hope that the standards will prove useful to the Biodiversity Informatics community. We would also thank all those who were involved as formal or public reviewers of these standards. Your input was greatly appreciated and was in various ways, incorporated into the final standards. These standards can be downloaded from http://www.tdwg.org/standards/150/download/. Chuck Miller TDWG Chair On behalf of the TDWG Executive Committee

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Request for proposal to draft a GBIF white paper on genomic data
by Éamonn Ó Tuama (GBIF) 10 Feb '11

10 Feb '11

[apologies for cross posting] GBIF has announced a call for proposals to draft a position paper on the publishing and discovery of, and access to, primary biodiversity data in the form of genomic level observations. Despite the ubiquity and importance of microbes, they are under-represented in the data published through the GBIF network. The sequencing of microbes directly from environmental samples (known as metagenomics, environmental genomics, ecogenomics, or community genomics) is revolutionising our understanding of microbial diversity in the natural environment and is set to take biodiversity informatics into the data-intensive eScience paradigm characterised by huge volumes of data delivered, in the main, as sensor-generated data streams. In addition, genetic barcoding will be a significant contributor to the genomic “data deluge”, including both observations that can be linked to named specimens as well as “operational taxonomic units” that are not. The focus of this call is on such metagenomic and barcoding data, identifying key activities that will enable GBIF and related communities of practice to participate fully in enabling the sharing and use of such data. Drawing on the needs of the relevant communities, the position paper will provide recommendations and an action plan on how to engage all players in creating a global infrastructure for the publishing and discovery of, and access to, genomic data and, in particular, address issues of interoperability and data integration. Further information on the call is available on the GBIF news site (http://www.gbif.org/communications/news-and-events/showsingle/article/gbif-…) including instructions for submitting an application. Please circulate the call to anyone you think may be interested in applying. With regards, Éamonn Ó Tuama _______________________________________________ Éamonn Ó Tuama, M.Sc., Ph.D. (eotuama(a)gbif.org) Senior Programme Officer, Inventory, Discovery, Access (IDA), Global Biodiversity Information Facility Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, DENMARK Phone: +45 3532 1494; Fax: +45 3532 1480

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Another Biodiversity informatics related position in Stockholm
by Torsten Eriksson 09 Feb '11

09 Feb '11

The Department of Biodiversity Informatics at the Swedish Museum of Natural History is searching for a biologist / content manager. Full time 1.5 years with a possible extension. The DINA project is an international collaborative software project dealing with the management of natural history collections (DINA: Digital information system for natural history collections). The project is run jointly by major museums in Sweden and is currently being extended to museums in the Nordic/Baltic countries. The position will be placed at the Swedish Museum of Natural History in Stockholm, Sweden. The successful candidate will work with museum curators and database managers – and their collection data – at partner institutions. The main focus will be to guide and help with the adaptation and transfer of currently available data into the DINA database, and to be a part of the planning, adaption and configuration of client workflows, based on local requirements. Another important task will be arranging DINA workshops and user education. Last day of application is 21 February 2011 (GMT+1). For more information about the project, see http://dina-project.net More info about the position and how to apply, see http://dina-project.net/pub/Main/DinaProjectNews/biologist.pdf Torsten Eriksson

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Re: [tdwg] tdwg Digest, Vol 48, Issue 2
by Poulos, Allison (Bioversity) 09 Feb '11

09 Feb '11

Sent from my iPhone On 09/feb/2011, at 12:00, "tdwg-request(a)lists.tdwg.org" <tdwg-request(a)lists.tdwg.org> wrote: > Send tdwg mailing list submissions to > tdwg(a)lists.tdwg.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.tdwg.org/mailman/listinfo/tdwg > or, via email, send a message with subject or body 'help' to > tdwg-request(a)lists.tdwg.org > > You can reach the person managing the list at > tdwg-owner(a)lists.tdwg.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of tdwg digest..." > > > Today's Topics: > > 1. GBIF KOS report published (?amonn ? Tuama (GBIF)) > 2. Beginner's guide to Persistent Identifiers published by GBIF > (?amonn ? Tuama (GBIF)) > 3. Biodiversity informatics position in Stockholm (Torsten Eriksson) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 9 Feb 2011 11:21:50 +0100 > From: ?amonn ? Tuama (GBIF) <eotuama(a)gbif.org> > Subject: [tdwg] GBIF KOS report published > To: <tdwg(a)lists.tdwg.org> > Message-ID: <00d101cbc843$29db19e0$7d914da0$@org> > Content-Type: text/plain; charset="iso-8859-1" > > The GBIF-commissioned white paper on Knowledge Organisation Systems (i.e., > Controlled Vocabularies, Ontologies, Thesauri, etc.) for biodiversity > informatics is now available at: > http://links.gbif.org/gbif_kos_whitepaper_v1.pdf. The white paper provides a > set of recommendations for consideration by GBIF and these are expected to > inform the development of the GBIF work programme, both in 2011 and in our > 3rd (2012-2016) five-year phase. > > > > Feedback on the white paper is welcomed. Please use the dedicated page > (http://community.gbif.org/pg/pages/view/11223/gbif-kos-report) of the KOS > Interest Group section > (http://community.gbif.org/pg/groups/11222/kos-interest-group/) on the GBIF > Community site. > > > > > > With regards, > > ?amonn ? Tuama > > > > > > _______________________________________________ > > ?amonn ? Tuama, M.Sc., Ph.D. (eotuama(a)gbif.org) > > Senior Programme Officer, Inventory, Discovery, Access (IDA), > > Global Biodiversity Information Facility Secretariat, > > Universitetsparken 15, DK-2100 Copenhagen ?, DENMARK > > Phone: +45 3532 1494; Fax: +45 3532 1480 > > > >

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Biodiversity informatics position in Stockholm
by Torsten Eriksson 09 Feb '11

09 Feb '11

The Department of Biodiversity Informatics at the Swedish Museum of Natural History is searching for a programmer / web developer. Full time two years with a possible extension. The DINA project is an international collaborative software project dealing with the management of natural history collections (DINA: Digital information system for natural history collections). The project is run jointly by major museums in Sweden and is currently being extended to museums in the Nordic/Baltic countries. The current position will be placed at the Swedish Museum of Natural History in Stockholm, Sweden. The successful candidate will join a small group of DINA developers that will develop efficient web clients and web services using a back-end SQL database. The web clients will be configured to the requirements of different museum departments. Last day of application is 21 February 2011 (GMT+1). For more information about the project, see http://dina-project.net More info about the position and how to apply, see http://dina-project.net/pub/Main/DinaProjectNews/programmer.pdf Torsten Eriksson

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Beginner's guide to Persistent Identifiers published by GBIF
by Éamonn Ó Tuama (GBIF) 09 Feb '11

09 Feb '11

GBIF is pleased to announce the publication of A Beginners Guide to Persistent Identifiers. Suggested citation: GBIF (2011). A Beginners Guide to Persistent Identifiers, version 1.0. Released on 9 February 2011. Authors Kevin Richards, Richard White, Nicola Nicolson, Richard Pyle, Copenhagen: Global Biodiversity Information Facility, 33 pp, accessible online at http://links.gbif.org/persistent_identifiers_guide_en_v1.pdf. With regards, Éamonn Ó Tuama _______________________________________________ Éamonn Ó Tuama, M.Sc., Ph.D. (eotuama(a)gbif.org) Senior Programme Officer, Inventory, Discovery, Access (IDA), Global Biodiversity Information Facility Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, DENMARK Phone: +45 3532 1494; Fax: +45 3532 1480

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GBIF KOS report published
by Éamonn Ó Tuama (GBIF) 09 Feb '11

09 Feb '11

The GBIF-commissioned white paper on Knowledge Organisation Systems (i.e., Controlled Vocabularies, Ontologies, Thesauri, etc.) for biodiversity informatics is now available at: http://links.gbif.org/gbif_kos_whitepaper_v1.pdf. The white paper provides a set of recommendations for consideration by GBIF and these are expected to inform the development of the GBIF work programme, both in 2011 and in our 3rd (2012-2016) five-year phase. Feedback on the white paper is welcomed. Please use the dedicated page (http://community.gbif.org/pg/pages/view/11223/gbif-kos-report) of the KOS Interest Group section (http://community.gbif.org/pg/groups/11222/kos-interest-group/) on the GBIF Community site. With regards, Éamonn Ó Tuama _______________________________________________ Éamonn Ó Tuama, M.Sc., Ph.D. (eotuama(a)gbif.org) Senior Programme Officer, Inventory, Discovery, Access (IDA), Global Biodiversity Information Facility Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, DENMARK Phone: +45 3532 1494; Fax: +45 3532 1480

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