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Digitiser posts in Denmark
by Pip Brewer 05 Jan '23

05 Jan '23

Hello, We are advertising for two Digitiser posts based at the Natural History Museum of Denmark (part of the University of Copenhagen) for DaSSCo (the Danish node of DiSSCo, an initiative to digitize all natural history specimens in Denmark). Please see the link below. Senior Digitiser for the Danish System of Scientific Collections (DaSSCo) (2 posts): https://jobportal.ku.dk/alle-opslag/?show=158214 The position is available from 1 April 2023 to 31 August 2026. Application closing date: 3 February 2026. Please help us spread the word on these posts! Social media, potential candidates, existing students, mailing lists etc - your help would be greatly appreciated! Best wishes, Pip Pip Brewer DaSSCo Project Leader University of Copenhagen Natural History Museum of Denmark Digital Collections København K pip.brewer(a)snm.ku.dk<mailto:pip.brewer@snm.ku.dk> [Logo for Københavns Universitet] How we protect personal data<https://informationssikkerhed.ku.dk/english/protection-of-information-priva…>

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Special Collections Researcher post at Cambridge University Herbarium (CGE): deadline 3rd Jan 2023
by Lauren Gardiner 23 Dec '22

23 Dec '22

** With apologies for cross-posting to multiple lists ** Dear All, Another year, another fantastic job opportunity at Cambridge University Herbarium! [?][?][?] We are recruiting a Special Collections Researcher to focus on identifying & mobilising our Type collections in 2023! [?] [?] [?] [?][?] Thanks to the Isaac Newton Trust we have 12 months' funding to support this post in the first instance, and the application deadline is 3rd January 2023 [?] [?] You can find out more about the project here: https://www.plantsci.cam.ac.uk/news/new-funding-help-university-herbarium-i… More details and further particulars for the post: https://www.jobs.cam.ac.uk/job/38536/ Please do share this message with colleagues, students, and your networks, newsletters, and job boards! Wishing you all a wonderful festive season and a very Happy New Year, Lauren --- Dr Lauren M. Gardiner FLS (pronouns: she/her)| Curator of the Cambridge University Herbarium (CGE) and Academic Librarian for the Department of Plant Sciences | CB2 1LR | Email: herbarium(a)plantsci.cam.ac.uk<mailto:herbarium@plantsci.cam.ac.uk> | @CUHerb<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftwitter.c…> | YouTube Channel<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.youtub…> This email (together with any files transmitted with it) is intended only for the use of the individual(s) to whom it is addressed and must not be distributed without explicit consent. It may contain information which is confidential and/or legally privileged. If you have received this email in error, please notify the sender by return email (or telephone) and delete the original message. Unless expressly stated, opinions in this email are those of the individual sender, and not of the University of Cambridge. The sender has taken reasonable precautions to check for viruses but the recipient opens this message at their own risk.

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Imageomics Institute Postdoctoral Research Associate search
by Bart, Henry L 21 Dec '22

21 Dec '22

The Tulane University Biodiversity Research Institute (TUBRI) is searching for a Postdoctoral Research Associate to involve in exciting, biology-guided, machine-learning research for two-years. The position is supported by a NSF Harnessing the Data Revolution Institute project entitled, Imageomics: A New Frontier of Biological Information Powered by Knowledge-Guided Machine Learning. This collaborative, multi-institution, multi-investigator project involves biologists and computer scientists who are training machine-learning algorithms to extract phenotypic trait data from images of a variety of types of biological specimens. The learning is aided by structured biological knowledge such as an anatomy ontology and phylogenetic trees. The postdoctoral researcher will contribute to ongoing efforts to extract trait data from images of fish specimens at the under the mentorship of Henry L. Bart Jr, Professor of Ecology and Evolutionary Biology and TUBRI Director, and Yasin Bakış, Senior Manager of Biodiversity Informatics and Data Engineering at TUBRI. The TUBRI postdoc will have opportunities to interact with other biologists, computer scientists, postdocs, and students from the ten other universities and research centers involved in the Imageomics Institute. TUBRI is a research center of Tulane's School of Science and Engineering, located on the grounds of the F. Edward Hebert Research Center in Belle Chasse, Louisiana, a suburb of New Orleans. TUBRI houses the Royal D. Suttkus Fish Collection and specializes in biodiversity discovery (primarily involving fishes) and biodiversity informatics research. The postdoctoral research associate will contribute to all aspects of ongoing work on the Imageomics Institute project at TUBRI, including: 1. Processing images of fish specimens and their supporting metadata to prepare them for machine-learning experiments; 2. Extracting data on morphological traits of fish specimens in images and determining the utility of the extracted data for identifying fish species and quantifying differences in traits of fish specimens from different populations within species; 3. Using extracted morphological traits data in "morphological barcoding" experiments focused on distinguishing images of fish specimens representing various fish taxonomic groups; 4. Verifying data and project output quality and accuracy; 5. Supporting the TUBRI coding team by a. assisting with software design where biological expertise is needed, b. making sure the software is properly documented, c. providing input during the coding process so that outputs are scientifically sound and publishable; 6. Attending project-related workshops, training programs, and meetings; 7. Keeping abreast of the latest literature relevant to the project; 8. Openly sharing findings with project collaborators; 9. Work collaboratively with Imageomics ML experts to explore develop new deep-learning methods; 10.Present analysis results at conferences and publish findings in scientific journals. Required Knowledge, Skills, and Abilities Prior (proven) experience in at least one of the following: Image Analysis, Artificial Intelligence, Genetic Algorithms, Biodiversity Informatics, Computational Biology, Bioinformatics, Biomedical Informatics, Ecoinformatics or a related field (scientific publications) Working knowledge of at least three of the following languages (one from each group) {Java, C, C++, C#}, {Python, PHP, Perl}, {R, Bash, JavaScript}, {ORACLE SQL, MSSQL, PostgreSQL, MySQL} Working knowledge of Unix based operating systems Experience in writing grant proposals and scientific publications Strong problem-solving skills Required Education and/or Experience PhD in Biological Sciences, Biodiversity Informatics, Computer Science, Information Sciences, Computational Biology/Bioinformatics, or a related field Preferred Qualifications Experience with: Image Processing Artificial Intelligence/Neural Networks Genetic Algorithms Web-database applications Experience in parallel computing (GPU) Working knowledge of version control system (GIT) Other Considerations The position is open to international candidates The postdoc is expected to travel internationally The postdoc should have strong communication and interpersonal skills Start date: As soon as an acceptable candidate is identified For additional information about the position, including application instructions, please contact Henry Bart (hbartjr(a)tulane.edu) or Yasin Bakiş (ybakis(a)tulane.edu) Henry L. Bart Jr., Ph.D. Director, Tulane University Biodiversity Research Institute Curator, Royal D. Suttkus Fish Collection 3705 Main Street, Belle Chasse, LA 70037 Voice: 504-394-1711; Fax: 504-394-5045 Professor of Ecology and Evolutionary Biology, Tulane University 400 Lindy Boggs Hall, New Orleans, LA 70118 Voice: 504-862-8283; Fax 504-862-8706 Website: http://people.tubri.org/hank/

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Imageomics Institute Graduate Research Assistant search
by Bart, Henry L 21 Dec '22

21 Dec '22

The Tulane University Biodiversity Research Institute (TUBRI) is searching for a Graduate Research Assistant (GRA) to involve in an exciting, research project entitled, Imageomics: A New Frontier of Biological Information Powered by Knowledge-Guided Machine Learning. TUBRI is a research center of Tulane's School of Science and Engineering, located on the grounds of the F. Edward Hebert Research Center in Belle Chasse, Louisiana, a suburb of New Orleans. TUBRI houses the Royal D. Suttkus Fish Collection and specializes in biodiversity discovery (primarily involving fishes) and biodiversity informatics research. The Imageomics Institute is collaborative, multi-institution, multi-investigator project involving biologists and computer scientists who are training machine-learning algorithms to extract phenotypic trait data from images of a variety of types of biological specimens. The learning is aided by structured biological knowledge such as an anatomy ontology and phylogenetic trees. The GRA will contribute to ongoing efforts at TUBRI to train computer algorithms to extract trait data from images of fish specimens. Interested persons must apply for admission to the Ph.D. program in Tulane's Department of Ecology and Evolutionary Biology (EEB) where they will develop and complete and original dissertation research project under the mentorship of Dr. Henry L. Bart Jr, Professor of Ecology and Evolutionary Biology and TUBRI Director, and Dr. Yasin Bakış, Senior Manager of Biodiversity Informatics and Data Engineering at TUBRI. The GRA position is funded for three years, but support guaranteed for up to 2-3 additional years of graduate study for completion of the Ph.D. degree. The GRA will also have opportunities to interact with other biologists, computer scientists, postdocs, and students from 10 other universities and research centers involved in the Imageomics Institute. Desired Knowledge, Skills, and Abilities Working knowledge of at least 2 of the following languages (one from each group) {Java, C, C++, C#}, {Python, PHP, Perl}, {R, Bash, JavaScript}, {ORACLE SQL, MSSQL, PostgreSQL, MySQL} Required Education and/or Experience BSc in Biology, Computer Science, Information Sciences, or a related field Should commit to complete PhD study in Ecology and Evolutionary Biology (EEB) or Interdisciplinary EEB and Computer Science Preferred Qualifications MSc in Biology, Computer Science, Information Sciences or a related field Working knowledge of Unix based operating systems Prior experience in one of the following fields: Image Processing, Artificial Intelligence, Genetic Algorithms, Biodiversity Informatics, Computational Biology, Bioinformatics, Biomedical Informatics, Ecoinformatics or a related field (publications) experience in Image Processing projects experience in Artificial Intelligence/Neural Networks projects experience in web-database applications experience in Genetic Algorithms Other requirement for the position Admission the Ph.D. program in Ecology and Evolutionary Biology at Tulane University The position is open to international candidates Should be able to travel internationally Strong communication and interpersonal skills Preferred Start Date: Fall 2023. Please use this link to apply for admission to the EEB Ph.D. program: https://applygrad.tulane.edu/apply/ For additional information or questions about the position please contact Henry Bart (hbartjr(a)tulane.edu) Henry L. Bart Jr., Ph.D. Director, Tulane University Biodiversity Research Institute Curator, Royal D. Suttkus Fish Collection 3705 Main Street, Belle Chasse, LA 70037 Voice: 504-394-1711; Fax: 504-394-5045 Professor of Ecology and Evolutionary Biology, Tulane University 400 Lindy Boggs Hall, New Orleans, LA 70118 Voice: 504-862-8283; Fax 504-862-8706 Website: http://people.tubri.org/hank/

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BioDigiCon: Final Update
by Nelson,Gil 15 Sep '22

15 Sep '22

BioDigiCon: Final Update Plans for the Biodiversity Digitization Conference (BioDigiCon 2022) are nearly complete. You can explore the agenda and other conference-related information on the conference wiki page here: https://www.idigbio.org/wiki/index.php/BioDigiCon_2022 and the presentation abstracts here: https://docs.google.com/document/d/1Qooo7bKfTC8mGXAct2xhjrhg1nWZFHPrtJBJ_n6…. Registration is free! Please register via Eventbrite: https://www.eventbrite.com/e/2022-biodigicon-tickets-367104919697 There is an excellent line-up of discussion sessions and workshops, including: BiotaPhy Webinar 2: Resolving Nomenclature: Making Appropriate Taxonomic Choices Maria Beatriz de Souza Cortez, University of Florida BioDigiCon is pleased to provide the platform for the second in a series of 10 webinars sponsored by BiotaPhy<https://www.idigbio.org/content/biotaphy-2022-webinar-series>, a set of computational workflows with broad impact on data-intensive research spanning ecology, phylogenetics, systematics, and conservation biology. Data quality: most common data dealbreakers Cat Chapman, iDigBio; Margot Schneider, Atlas of Living Australia; Dora Canhos, CRIA; Andrea Hahn, GBIF; Elspeth Haston, RBGE Digital Extended Specimen Discussion Session Libby Ellwood, iDigBio; Katja Seltmann, Cheadle Center for Biodiversity and Ecological Restoration, UC Santa Barbara; Julie Allen, University of Nevada, Reno; Katie Pearson and Ed Gilbert, Symbiota Support Hub Digitization Coordination: Combining Project Management & Digitization Efforts to Benefit Collections, Big and Small Jackie Chapman, Smithsonian Libraries and Archives; Frederik Berger, MfN Berlin; Helen Hardy, NHM London; Sylvia Orli, NMNH Smithsonian; Mareike Petersen, MfN Berlin; Kira Sobers, Smithsonian Libraries and Archives; Alyson Wilkins, NHMU Utah Digitization Workflows in Symbiota-based Biodiversity Specimen Data Portals Katie Pearson, Symbiota Support Hub, Arizona State University; Lindsay Walker, Symbiota, ASU GBIF, ALA, iDigBio: Aligning systems to benefit data mobilization Federico Mendez (GBIF), Javier Molina (ALA), Maureen Kelly (iDigBio), Chris Wilson (IDigBio) Imaging Biodiversity Specimens: First Steps to a Great Start (and Beyond) Austin Mast, Florida State University, Dept of Biological Science; Lauren Cohen, FSU, Institute for Digital Information and Scientific Communication; Nicole James, FSU, Institute for Digital Information and Scientific Communication; Alex Adkinson, FSU, Department of Art Including Indigenous Metadata in Collection Records Maui Hudson, University of Waikato; Jane Anderson, New York University Solutions for long-term image storage and accessibility Dave Blackburn, University of Florida; Doug Boyer, Duke University; Nico Franz, Arizona State University; Michelle Koo, University of California - Berkeley; Nelson Rios, Yale University; Julie Winchester, Duke University Sustaining Institutional Digitization of Biodiversity Collections: Considerations and Examples Austin Mast (iDigBio, FSU), David Jennings (iDigBio), Jenn Yost (Symbiota Support HUB, CalPoly), Lindsay Walker (Symbiota Support HUB, ASU) Capturing trait data: broad, across different taxonomic groups Rob Guralnick, Florida Museum of Natural History; Maggie Hantak, FLMNH; Ed Stanley, FLMNH; Julie Allen, University of Nevada at Reno; Jacob Idec, FLMNH; Bryan McLean, University of North Carolina, Greensboro Gil Nelson, PhD Director, Integrated Digitized Biocollections (iDigBio) President, Natural Science Collections Alliance (NSCA) Florida Museum of Natural History University of Florida gnelson(a)floridamuseum.ufl.edu

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BiotaPhy Webinar Series
by Nelson,Gil 14 Sep '22

14 Sep '22

BiotaPhy Hi everyone, Do you want to learn how to use occurrence data and available software to address questions in ecology and evolutionary biology but haven’t had a chance to take a course and are overwhelmed by the options for self-teaching? Would you like to incorporate this sort of research into your classes but don’t have time to create the materials and examples? If either of these applies, then join the BiotaPhy Project for an upcoming series of 10 webinars designed to take you from biological question to data acquisition and cleaning to analysis and interpretation! BiotaPhy is a collaboration among iDigBio, the Open Tree of Life, and Lifemapper projects and personnel. We have converted our popular summer workshop into a webinar series; see below for topics. Webinars will be held Wednesdays at 12:30 pm Eastern time, beginning September 21. All webinars will be recorded and made available, so you won’t get behind if you need to miss a session. The schedule is: Webinar 0: Terms, Concepts, Data Formats – A Tutorial for Background Available online at the registration page [coming soon!] Webinar 1: Introduction: Scope and Research Potential for Multidisciplinary Biodiversity Modeling and Analysis Date: 09/21/2022 Webinar 2: Resolving Nomenclature: Making Appropriate Taxonomic Choices Date: 09/28/2022 Webinar 3: Clean Your Dirty Data Date: 10/05/2022 Webinar 4: Georeferencing with GEOLocate Date: 10/12/2022 Webinar 5: Big Data Munging (a.k.a Splitting and Merging Occurrence Data by Taxa from Multiple Sources) Date: 10/19/2022 Webinar 6: Species Distribution Modeling 1 Date: 10/26/2022 Webinar 7: Species Distribution Modeling 2 Date: 11/02/2022 Webinar 8: Introducing Presence-Absence Matrices for Large Scale Analyses Date: 11/9/2022 Webinar 9: Phylogenetic Diversity: Integrating Phylogenies with Species and Biogeographic Data Date: 11/16/2022 Webinar 10: Hypothesis Testing and Randomization Date: 11/30/2022 To register, please go to https://ufl.zoom.us/meeting/register/tJclfuCtrDwjE9PnPXJYkiSnglbnNd_BYCS4. Note that you will need to register separately for each week so that we can plan for weekly attendance. And for more information, visit https://www.idigbio.org/content/biotaphy-2022-webinar-series<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.idigb…> Please share with your networks, and sorry for cross-postings! Hope to see you soon! Best, Pam ----- Pamela S. Soltis (she/her/hers) Director, UF Biodiversity Institute Distinguished Professor and Curator Laboratory of Molecular Systematics and Evolutionary Genetics Florida Museum of Natural History Dickinson Hall University of Florida Gainesville, FL 32611 Phone: (352) 273-1964 Fax: (352) 846-2154 Email: psoltis(a)flmnh.ufl.edu<mailto:psoltis@flmnh.ufl.edu>

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automated response
by Christy Semmens 05 Aug '22

05 Aug '22

Thank you for your message. I am currently out of the office with little to no internet access until August 8. If you have an immediate need, please contact martha(a)REEF.org. Otherwise, I will get back with you as soon as I am able.

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Biodiversity Digitation Conference Lightning Rounds: Register Now
by Nelson,Gil 05 Aug '22

05 Aug '22

We are pleased to announce a sampling of the lightning rounds to be offered at BioDigiCon. Remember, registration is free, and all events will be pre-recorded or recorded live for asynchronous viewing to suit your time zone or schedule. Registration is free but required. Register here: https://www.eventbrite.com/e/2022-biodigicon-tickets-367104919697<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.eventbrite.com_e_2…> Lightning Rounds: Up to 30 rounds will be offered. Here is a sampling: A set of four rounds focusing on comparing popular collections management systems (CMS) for folks deciding which CMS to adopt, determining whether to switch from a custom CMS, adopt a new CMS, or just to learn more of these options. Talks will be followed by a 10-minute Q&A. Included are: * Arctos, with Emily Braker, University of Colorado * Emu, with Larry Gall, Yale University * Specify, with Randy Singer, University of Michigan * Symbiota, with Katie Pearson, California Polytechnic State University A set of five rounds focusing on digitization activities at the U.S. National Museum of Natural History, Smithsonian. * Coordinating digitization at NMNH, Sylvia Orli * A completely digitized collection – what does digitization maintenance look like for NMNH botany, Sylvia Orli * Digitizing the Odonata, Torsten Dikow * Creating an Informatics and Data Science Center, Rebecca Snyder * New generation digitization of specimens in situ, Holly Little Individual lightning rounds will include: * Extending the model for digitized data, Ely Wallis * Software-based capture of 2D barcodes on duplicate herbarium sheets during digitization & subsequent data discovery via GBIF, including a sample script to adapt and reuse, David Shorthouse & Shannon Asencio, Agriculture and Agri-Food Canada / Government of Canada * Digitization as art, Zach Randall, Florida Museum of Natural History * Global Biotic Interactions (GloBI), Jorrit Poelen, Cheadle Center for Biodiversity & Ecological Restoration * A workflow for cleaning Notes from Nature data transcriptions, Peter Oboyski, Essig Museum * Digitizing the CSIRO Collections, Australia, Nicole Fisher, CSIRO * An open, continuously updated Fern Tree of Life, Joel Nitta, University of Tokyo * 10 minute Q&A with U.S. National Science Foundation representatives, Steve Ellis * MorphoBank, Brooke Long-Fox * [https://lh5.googleusercontent.com/ob3hAcrMNxtR4nN6wVJx-9ZBN9V0JkjX0eeslXshB…]

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automated response
by Christy Semmens 20 Jul '22

20 Jul '22

Thank you for your message. I am currently out of the office with little to no internet access until August 8. If you have an immediate need, please contact martha(a)REEF.org. Otherwise, I will get back with you as soon as I am able.

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Digitisation Data Lead / Consultant
by Pip Brewer 14 Jul '22

14 Jul '22

We are seeking project support (a Data Lead or Data Consultant) to help develop and deploy our IT infrastructure for the Danish Natural History specimen digitization program (DaSSCo). This can be in the form of an official collaboration, consultancy or direct employment on a part-time or full-time basis of limited duration (at least initially). We are also open to solutions which blend off-site working and face-to-face meetings. Our main priority is finding someone who has the skills we need and can integrate easily into the existing team. Our initial needs are focused on: * Implementation of the data architecture needed for the DaSSCo digitization program * Implementation of middleware which stores image metadata and controls access to images * Designing and facilitating implementation of a specimen data refinery * Recommendations on and help to implement solutions for associating Persistent Identifiers with digital data * Documentation of all processes and decisions * Liaison and effective communication with the project team and other stakeholders The aim of DaSSCo is to digitize all natural history specimens in Denmark through a co-ordinated effort. The first 5 years of this long-term program are being financed by the Danish Ministry of Higher Education and Science, where the focus is to set up the infrastructure and workflows and to start mass digitization efforts. The program officially started on 1st September 2021 and we will be commencing digitization itself at the start of 2023. As the program is already underway, we are looking for the Data Lead or Data Consultant to start as soon as possible. You should have experience with software development and programming, preferably in Python, and you should be a proficient Linux / Unix users, preferably with experience with administration of such systems. We would love to chat further if you or someone from your team, has the relevant skills and experience and would be interested in working with us. You can contact the DaSSCo team directly by emailing Pip Brewer (pip.brewer(a)snm.ku.dk<mailto:pip.brewer@snm.ku.dk>) and Kim Steenstrup Pedersen (kimstp(a)di.ku.dk<mailto:kimstp@di.ku.dk>). Pip Brewer DaSSCo Project Leader University of Copenhagen Natural History Museum of Denmark Digital Collections København K DIR +45 35 33 42 41 pip.brewer(a)snm.ku.dk<mailto:pip.brewer@snm.ku.dk> [Logo for Københavns Universitet] How we protect personal data<https://informationssikkerhed.ku.dk/english/protection-of-information-priva…>

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