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EOL funds SPM work by Plazi
by Eamonn O Tuama 30 Jul '08

30 Jul '08

Dear TDWG Members, I am very pleased to announce the awarding of a contract to Dr Donat Agosti of Plazi (www.plazi.org) to undertake work on the Species Profile Model (SPM). With funding from Encyclopedia of Life (EOL - www.eol.org), Plazi will develop an SPM extension module as an addendum to their 2007 GBIF Seed Money Award project entitled "Extracting Nomenclatural Data, Species Descriptions and Collecting Events from Legacy Publications: The Zootaxa-TaxonX-ZooBank Project" (GBIF Tracking Number 2007-94). The latter provides, as one of its outputs, biodiversity literature encoded as TaxonX XML documents through the use of the GoldenGate markup tool. The SPM extension will provide XSLT scripts for the creation of SPM documents expressed in RDF from the TaxonX documents. The RDF files will be mounted on the Plazi web server for harvesting by SPM aware agents, particularly those to be created by the EOL project. SPM data will be served through TAPIR. This work will be done in close cooperation with GBIF and will engage the wider community through use of the SPM wiki site (http://wiki.tdwg.org/SPM) and mailing list (tdwg-spm-owner(a)lists.tdwg.org) hosted by TDWG. Other parties will be assisted in exposing species data contained in literature through documenting the process of using the freely accessible GoldenGate tools to provide SPM encoded data. The results of the project will also be presented in the SPM session at the TDWG 2008 conference. If you are interested in participating in developments around SPM, please join the TDWG SPM maining list (tdwg-spm(a)lists.tdwg.org) and keep an eye on the SPM wiki (http://wiki.tdwg.org/SPM/). Best regards, Éamonn -- Éamonn Ó Tuama, Ms.C., Ph.D. (eotuama(a)gbif.org), Senior Programme Officer - Inventory, Discover, 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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FW: ALA Newsletter 1
by Lee Belbin 14 Jun '08

14 Jun '08

I thought this first ALA Newsletter was well worth posting to the lists. Lee Belbin TDWG Secretariat From: Donald.Hobern(a)csiro.au [mailto:Donald.Hobern@csiro.au] Sent: Friday, 13 June 2008 10:15 AM To: Donald.Hobern(a)csiro.au Subject: ALA Newsletter 1 Atlas of Living Australia Newsletter 1 (10 June 2008) Welcome to the Atlas of Living Australia newsletter The Atlas of Living Australia project is now making progress and we plan to produce a regular informational newsletter to keep stakeholders and friends aware of what is happening. We would appreciate it if you could pass this first newsletter on to interested colleagues. Please send an email to Wolf Wanjura ( <mailto:Wolf.Wanjura@csiro.au> Wolf.Wanjura(a)csiro.au) if you wish to be added to the mailing list for this newsletter, or if you wish to be removed from the list. The project The Atlas of Living Australia (ALA) is a five-year project funded under the Australian Government's National Collaborative Research Infrastructure Strategy ( <http://www.ala.org.au/ncris.htm> NCRIS) and involving a wide range of Australian scientific institutions and organisations (see <http://www.ala.org.au/participants.htm> http://www.ala.org.au/participants.htm). The goal of the project is to develop web-based tools to enable users to discover, access and use the widest possible range of information resources relating to Australia's fauna and flora, including databases from natural history collections and ecological field work, images and other multimedia, text documents, identification tools and molecular data. A presentation giving an overview of some of the planned project activities can be found at <http://www.ala.org.au/documents.htm> http://www.ala.org.au/documents.htm ( <http://www.ala.org.au/docs/ALAChallengesAndOpportunities.ppt> PowerPoint, 11.5MB; <http://www.ala.org.au/docs/ALAChallengesAndOpportunities.pdf> PDF, 2.3MB) ALA web site The ALA has launched its web site ( <http://www.ala.org.au/> http://www.ala.org.au/). At present it mostly comprises information about the project and its participant organisations, but the site will increasingly include information and discussions on the planning and implementation of the project. Ultimately it will become the ALA portal for discovering information on all Australian species. ALA user needs analysis What can you do for the ALA today? We need your contacts in biodiversity - lots of them, and from as many different fields as you can identify. We want to ask them (and you) a few simple questions. We have commissioned a small team to investigate how users access such information today and how they use it in their own studies and decision-making. Over the next few months, this team will be contacting many of you to learn more about your needs. Please give them your support - we want to understand how the ALA can become a useful tool for you in your work. For more information on this process, see <http://www.ala.org.au/userneedsanalysis.htm> http://www.ala.org.au/userneedsanalysis.htm. TDWG 2008 conference to be held in Perth TDWG, the international biodiversity information standards organisation ( <http://www.tdwg.org/> http://www.tdwg.org/), will hold its annual conference at the Western Australian Maritime Museum, Perth, 19-25 October 2008. One day of the conference will be devoted specifically to the Atlas of Living Australia and will include workshops to explore ways for the project to meet the needs of Australian researchers. For more information on the conference, see <http://www.ala.org.au/tdwg2008.htm> http://www.ala.org.au/tdwg2008.htm. ALA review of online and desktop tools Paul Flemons and John Tann from the Australian Museum have carried out an extensive review of software components which could feed into the development of the Atlas or which could be of benefit to data providers or users. The results of this review are online at <http://alatools.pbwiki.com/> http://alatools.pbwiki.com/. Please take a look at this resource and suggest any additional tools which should be included. For more information on this review, see <http://www.ala.org.au/toolsurvey.htm> http://www.ala.org.au/toolsurvey.htm. ALA and GBIF We have started discussions with the Global Biodiversity Information Facility (GBIF, <http://www.gbif.org/> http://www.gbif.org/) to ensure that the ALA can act as the Australian node within GBIF. The ALA expects to reuse code from the GBIF Data Portal to develop its own cache of Australian biodiversity records. This cache will then serve as an efficient way to integrate Australian data into GBIF's global network. The ALA has also begun discussions with GBIF New Zealand on possible ways to share resources and align activity. Other activity Over the last few months the ALA team has been working on the following tasks: * Establishing the ALA web site * Interviewing candidates for the positions of ALA Architect, Metadata Curator and Java Developer * Developing the ALA's 2008-2009 Business Plan * Working with the <http://www.ala.org.au/ncris.htm> NCRIS Platforms for Collaboration capability's <http://www.ncris.dest.gov.au/capabilities/collaborative_investment_plan_pla tforms.htm#National_eResearch_Architecture_Taskforce_(NeAT)> NeAT programme to plan the development of the ALA's Metadata Repository and Data Annotation Services. * Meetings to explore possible collaborations with related organisations and projects, including contacts with representatives from Birds Australia, CSIRO Publishing, EarthWatch, GBIF New Zealand, the Murray Darling Basin Commission, Rio Tinto, the Subcommittee on Plant Health Diagnostic Standards and many of the ALA <http://www.ala.org.au/participants.htm> participants.

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Fwd: Biodiversity Informatics/Conservation Planning Specialist for Madagascar (with attachment)
by John R. WIECZOREK 11 Jun '08

11 Jun '08

---------- Forwarded message ---------- From: Claire Kremen <ckremen(a)gmail.com> Date: Jun 10, 2008 3:24 PM Subject: Biodiversity Informatics/Conservation Planning Specialist for Madagascar (with attachment) To: *Dear Colleagues* *Please circulate widely! Best wishes, Claire Kremen * * * *Biodiversity Informatics/Conservation Planning Specialist for Madagascar* *University** of California**, Berkeley* * * The *Reseau de la Biodiversite de Madagascar* (REBIOMA), joint project of University of California and Wildlife Conservation Society, works to support science-based marine and terrestrial conservation planning, through creation of a web-based biodiversity information system, capacity building, and development of conservation plans. We seek a scientist to provide technical support for conservation planning (marine and terrestrial); contribute to development of the REBIOMA web-portal; build capacity of the REBIOMA team; conduct grant management and project coordination. One year position (renewable contingent upon funding) available as soon as Aug 1, 2008, at the Assistant or Associate Specialist level (salary commensurate with experience ($38952 - $48372), reporting to Prof. Claire Kremen. Advanced degree in environmental field; experience in GIS, conservation planning and/or biodiversity informatics. Successful candidate should have experience in project management, good interpersonal skills, knowledge of French, and willingness to spend significant time in Madagascar. * * Submit a CV, brief letter, and names and contacts of 3 references to Jeanne G. Kassis (Position #101, Berkeley Natural History Museums, 3101 Valley Life Science Building, UC Berkeley, CA 94720 or by email attachments to kassj(a)berkeley.edu by July 26, 2008. Further information about the position and project is available at http://nature.berkeley.edu/kremenlab/kremen_research.html and attached.. The University of California, Berkeley, is an Equal Opportunity Employer committed to excellence through diversity. -- Claire Kremen Assistant Professor Environmental Sciences Policy and Management 137 Mulford Hall University of California Berkeley, CA 94720-3114 510-643-6339 Fax 510-642-7428 http://nature.berkeley.edu/kremenlab/ http://www.berkeley.edu/news/media/releases/2008/04/10_madagascar.shtml http://www.kqed.org/quest/television/view/434 http://www.sfgate.com/cgi-bin/article.cgi?f=/c/a/2008/04/12/MNU710263B.DTL

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Moving forward with Species Profile Model
by Eamonn O Tuama 06 Jun '08

06 Jun '08

Dear TDWG Members, Much was achieved for the Species Profile Model over quite a short period in 2007 but we need to ensure that development continues, and, in particular, that the SPM is actually tested in some real world applications so we can learn how to refine and enhance it. I am very happy to report that the first test case will commence soon when Plazi.org starts making species level information available as SPM compatible RDF data from documents processed through the GoldenGate/TaxonX system, and with EOL as the first client for such data. We hope that this will encourage others to also use the SPM for sharing species level information and/or to use such data in novel applications. What next for SPM in the TDWG context? I would highlight the following: 1. consider formally establishing SPM as a task under the Biological Descriptions Interest Group in order to take it forward through the TDWG standards process; 2. identify a champion for SPM who will take it forward; 3. continue to use the TDWG wiki (http://wiki.tdwg.org/SPM/) as a focal point for sharing information, but 4. also use the SPM mailing list (tdwg-spm(a)lists.tdwg.org) hosted by TDWG so that we will have an online archive of discussions; 5. create a core SPM group (open to all) which is credited on the SPM wiki; 6. task the SPM group with the main goal of developing a summary document with review/recommendations on how to move forward on SPM. So, let me know if you are interested in participating in the SPM task group. In addition, as a first essential step, please join the TDWG SPM maining list (tdwg-spm(a)lists.tdwg.org) and keep an eye on the SPM wiki (http://wiki.tdwg.org/SPM/). Best regards, Éamonn ________________________________________________________________ Éamonn Ó Tuama, Ph.D. (eotuama(a)gbif.org), Senior Programme Officer for 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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TDWG 2008 in Fremantle, Western Australia
by Lee Belbin 03 Jun '08

03 Jun '08

Registration for TDWG 2008 is now open at www.TDWG.org/conference2008/registration. The conference will be held at the Maritime Museum of Western Australia in Fremantle, about 20km southwest of Perth. Details about the conference can be found on the TDWG site at http://www.tdwg.org/conference2008/. Note: The AUS$80 discount for registration will expire September 6. There is a wide range of accommodation available in Fremantle within easy walking distance to the museum. But, as Fremantle is small, there is not a lot of any one type of accommodation available. The 4.5 star Esplanade Hotel has discounted rates for the conference (quote "Biodiversity of Information Standards 2008"). A cost-effective option for Fremantle is to share a house or apartment. Most of these are close to the venue but you will have to book quickly as there are only a limited number available. Please see http://www.tdwg.org/conference2008/accommodation/ for all conference details and use our Wiki http://wiki.tdwg.org/twiki/bin/view/Conferences/SharedAccommodation to help find others who could share accommodation with you. The outline of the conference program can be found at http://www.tdwg.org/conference2008/program. Session Chairs are being identified and are now seeking presenters. If you wish to present an oral presentation, a poster or a computer-based demonstration, please contact the relevant Session Chair as soon as possible as they will be identifying speakers for their sessions. The program this year will centre around a the Atlas of Living Australia (Wednesday October 22). TDWG is keen to understand and to support this significant project. There is also a number of tutorials (session 8 and repeated session 13) that are aimed at presenting key TDWG activities in simple terms. Early registration for these tutorials would be appreciated. Please contact Adrian Rissone (a.rissone(at)nhm.ac.uk) for any other program details and lee(at)tdwg.org <mailto:lee@tdwg.org> for any other information. Lee Belbin TDWG Secretariat

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Biological Taxonomy Vocabulary 0.1
by Andy Mabbett 03 Jun '08

03 Jun '08

A friend writes: Unable to find a vocabulary that was satisfactory for my needs, I've put together a simple vocabulary for biological taxonomy. The idea is to make it powerful enough to cover 80% of use cases, but still simple for most non-expert biologists to use. Namespace and spec is: http://purl.org/NET/biol/0.1/ You can read his full post, and subsequent discussion, at: <http://lists.w3.org/Archives/Public/semantic-web/2008May/thread.html#msg45> (aka <http://tinyurl.com/575w25>) (Also posted to ttaxacom(a)mailman.nhm.ku.edu) -- Andy Mabbett

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Re: [tdwg] tdwg Digest, Vol 16, Issue 2
by Alina Freire-Fierro 19 May '08

19 May '08

Hi: I am attending the SPNHC Meetings in Oklhahoma City during May 13-18. I will take care of everything related with the herbarium (including inquiries and loans) upon my return. If it is really urgent, please contact Amanda Labadie (labadie(a)ansp.org) or Elana Benamy (benamy(a)ansp.org). Or else, please try my personal e-mail (alina_ff(a)yahoo.com). I might be able to check it once in a while. Many thanks! Alina

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FW: CDL releases eXtensible Text Framework (XTF) 2.1
by Neil Thomson 19 May '08

19 May '08

May be of interest to TDWG list members ... Neil ------- Neil Thomson Head of Data & Digital Systems The Natural History Museum, Cromwell Road, London SW7 5BD Tel: +44 (0)20 7942 5294, Fax: +44 (0)20 7942 5559, Email: n.thomson(a)nhm.ac.uk http://www.nhm.ac.uk <http://www.nhm.ac.uk/> ________________________________ From: Metadata Encoding and Transmission Standard [mailto:METS@loc.gov] On Behalf Of Lisa Schiff Sent: 13 May 2008 22:09 To: METS(a)LISTSERV.LOC.GOV Subject: [METS] CDL releases eXtensible Text Framework (XTF) 2.1 **This announcement is being sent to many lists; apologies in advance for duplication.** FOR IMMEDIATE RELEASE Contact: Lisa Schiff California Digital Library University of California, Office of the President 415 20th St., 4th Floor Oakland, CA 94612 (510) 587-6132 lisa.schiff(a)ucop.edu http://www.cdlib.org/inside/projects/xtf/ California Digital Library Announces New Release of the eXtensible Text Framework (XTF) Oakland, CA, May 12, 2008 - The California Digital Library (CDL) is pleased to announce a new release of its search and display technology, the eXtensible Text Framework (XTF) <http://www.cdlib.org/inside/projects/xtf/> version 2.1 (http://www.cdlib.org/inside/projects/xtf/ ). XTF is an open source, highly flexible software application that supports the search, browse and display of heterogeneous digital content. XTF offers efficient and practical methods for creating customized end-user interfaces for distinct digital content collections. Highlights from the 2.1 release include: * Extensive interface improvements, including new search forms, built-in faceted browsing, and a new look and feel. * Increased support for document and information exchange formats. * XHTML and OAI-PMH output * NLM article format indexing and output * Microsoft Word indexing * Streamlined XSLT stylesheets for simpler deployment and adaptation. * Updated documentation that has been moved to the XTF project wiki <http://xtf.wiki.sourceforge.net/> , allowing XTF implementers to share solutions with entire user community. * "Freeform" Boolean query language, offered as an experimental feature. * Backward compatibility with existing XTF implementations. A complete list of changes <http://xtf.wiki.sourceforge.net/changeLog_2.1> is available on the XTF Project page on SourceForge <http://sourceforge.net/projects/xtf/> , where the distribution (including documentation) can also be downloaded. Since the first deployment of XTF in 2005, the development strategy has been to build and maintain an indexing and display technology that is not only customizable, but also draws upon tested components already in use by the digital library and search communities - in particular the Lucene text search engine, Java, XML, and XSLT. By coordinating these pieces in a single platform that can be used to create multiple unique applications, CDL has succeeded in dramatically reducing the investment in infrastructure, staff training and development for new digital content projects. XTF offers a suite of customizable features that support diverse intellectual access to content. Interfaces can be designed to support the distinct tools and presentations that are useful and meaningful to specific audiences. In addition, XTF offers the following core features: * Easy to deploy: Drops directly in to a Java application server such as Tomcat or Resin; has been tested on Solaris, Mac, Linux, and Windows operating systems. * Easy to configure: Can create indexes on any XML element or attribute; entire presentation layer is customizable via XSLT. * Robust: Optimized to perform well on large documents (e.g., a single text that exceeds 10MB of encoded text); scales to perform well on collections of millions of documents; provides full Unicode support. * Extensible: * Works well with a variety of authentication systems (e.g., IP address lists, LDAP, Shibboleth). * Provides an interface for external data lookups to support thesaurus-based term expansion, recommender systems, etc. * Can power other digital library services (e.g., XTF contains an OAI-PMH data provider that allows others to harvest metadata, and an SRU interface that exposes searches to federated search engines). * Can be deployed as separate, modular pieces of a third-party system (e.g., the module that displays snippets of matching text). * Powerful for the end user: * Spell checking of queries * Faceted displays for browsing * Dynamically updated browse lists * Session-based bookbags These basic features can be tuned and modified. For instance, the same bookbag feature that allows users to store links to entire books, can also store links to citable elements of an object, such as a note or other reference. A sampling of XTF-based applications both within and outside of the CDL include: * Mark Twain Project Online <http://www.marktwainproject.org/> (http://www.marktwainproject.org), developed by the Mark Twain Papers Project, the CDL and the University of California Press. * Calisphere <http://www.calisphere.org/> (http://www.calisphere.org/), a curated collection of primary sources keyed to the curriculum standards of California's K-12 community, developed by the CDL. * The Encyclopedia of Chicago <http://www.encyclopedia.chicagohistory.org/> (http://www.encyclopedia.chicagohistory.org/), developed by the Chicago History Museum, The Newberry Library, and Northwestern University * The Chymistry of Isaac Newton <http://webapp1.dlib.indiana.edu/newton/> (http://webapp1.dlib.indiana.edu/newton/) and The Swinburne Project <http://webapp1.dlib.indiana.edu/swinburne/www/swinburne/> (http://webapp1.dlib.indiana.edu/swinburne/www/swinburne/), Indiana University * Finding Aides at the New York Public Library <http://labs.nypl.org/2007/10/30/extensible-text-framework-xtf/> (http://labs.nypl.org/2007/10/30/extensible-text-framework-xtf/) * EECS Technical Reports <http://sunsite2.berkeley.edu:8088/xtf/servlet/org.cdlib.xtf.crossQuery. CrossQuery?rmode=btr> (http://sunsite2.berkeley.edu:8088/xtf/servlet/org.cdlib.xtf.crossQuery. CrossQuery?rmode=btr), UC Berkeley ### ----------------------------------------------- Lisa Schiff, Ph.D. Technical Lead, Publishing California Digital Library 300 Lakeside Drive #745 Kaiser Center Oakland, CA 94612 510-987-0881 (t) 510-987-0243 (f) www.cdlib.org <http://www.cdlib.org/> lisa.schiff(a)ucop.edu

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Multimedia Resources in Biodiversity - Survey launched
by Donald.Hobern＠csiro.au 05 May '08

05 May '08

GBIF has recently established a Multimedia Resources Survey Task Group ( http://www.gbif.org/News/NEWS1205258694). The Task Group has now commissioned a Survey of Multimedia Resources in Biodiversity. This survey is now open for responses at http://www.surveymonkey.com/s.aspx?sm=3IfGMGfEI3SMm_2f5h3yNuAw_3d_3d. More information on the survey can be found at http://www.gbif.org/News/NEWS1209648731. I would encourage TDWG participants to contribute to this survey. Many thanks, Donald Donald Hobern, Director, Atlas of Living Australia CSIRO Entomology, GPO Box 1700, Canberra, ACT 2601 Phone: (02) 62464352 Mobile: 0437990208 Email: Donald.Hobern(a)csiro.au

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TDWG mid-year message
by Donald.Hobern＠csiro.au 21 Apr '08

21 Apr '08

*** I apologise to those who receive this by multiple routes. *** Dear TDWG Members and Friends, We are just about at the mid-point between TDWG annual meetings and activity within subgroups is at a natural low. This is however a good time to review the status of all our projects and activities and to try to identify the key things we would like to see happen during the rest of the year. Biodiversity Informatics remains an active and developing area of research and we are getting closer to supporting a new generation of biodiversity data applications. The recent launch of the Encyclopedia of Life demo pages is a powerful reminder of several things. First, there is a great interest in marshalling information on the world's biodiversity. Secondly, there is an enormous need for us to find new and faster ways to bring large quantities of high-quality data online. Thirdly, we still have plenty of work ahead of us in finding better ways to make all of these data interoperate freely so that they can become part of a rich and developing store of knowledge. TDWG has a critical role to play in ensuring that all this happens in a well-structured way. TDWG is joining with a wide range of other biodiversity informatics organisations to plan the e-Biosphere conference to be held in London in 2009. This meeting is intended to showcase what is happening in our field and we must consider what we would most like to have demonstrated in such a forum. What are the big applications which our wider community could soon deliver to support science and sound policy? What tools would we like to be able to put in the hands of researchers, administrators or the general public? What do we need to start doing now to make these possible? I am of course facing these same questions in the Australian context. When I consider the key areas where the Atlas of Living Australia (ALA) needs to make rapid progress, TDWG has a significant role to play in all of them. Some particular focus areas include: * Improving the quality and management of metadata - the ALA needs a metadata repository to manage information on biodiversity data sets and will be seeking to develop a repository which is compatible both with other national repositories and also with international developments in biodiversity informatics * Lowering the technical threshold for sharing biodiversity data in structured forms - the ALA will be exploring ways to package provider software tools as bundles requiring minimal configuration (and will explore offering a centralised installation of these tools for those who do not wish to maintain a web server) * Developing tools to support online identification - we need to find efficient ways to exploit structured descriptive data where it is available. We also need to supplement these data with well-organised access to the original literature, images, distribution data, etc. in an environment which guides users to the best identifications possible. * Managing data on species interactions - I believe that the most significant class of data we do not handle today is information on the trophic and other relationships between taxa. Many new applications, and new ways to navigate biodiversity data, would become feasible if we could organise what is known in the literature of predator-prey, host-parasite, pollinator-plant and other relationships. I would really like to explore text mining or other approaches as routes to developing significant databases of such information. These are some of the areas where I would like us to make progress. What would you add to this list? Finally, I must make an apology. At the TDWG meeting in Bratislava, I made a call for those who would be interested in collaborating on developing a Java implementation of TAPIR. Unfortunately I failed to do anything about this in all the business of moving out to Australia. I do however still know of a couple of groups who would like to do this. If you have an interest in a Java TAPIR implementation, and could contribute to making it happen, please let me know (again) and I will try to get everyone concerned in contact with each other. Very best wishes, Donald Donald Hobern, Director, Atlas of Living Australia CSIRO Entomology, GPO Box 1700, Canberra, ACT 2601 Phone: (02) 62464352 Mobile: 0437990208 Email: Donald.Hobern(a)csiro.au

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