Archive for the ‘phyloinformatics’ Category

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the latest news…

Wednesday, April 28th, 2010

mystery wasp

I haven’t posted any news about the Museum in what seems like FOREVER. So here’s what’s been happening, in short snippets, during the last couple months:

  • In March I traveled to South Australia to talk about ongoing projects (and hash out future research ideas) with my colleagues John Jennings and Andy Austin. We traveled 1200 km or so through eastern SA and western VIC, collecting along the way. I’ll write a separate post about this adventure, complete with pictures and more details. In the meantime, see if you can figure out what this mystery wasp (above) is and where/how it was collected!
  • World-class Hymenoptera morphologists Gary Gibson and Lars Vilhelmsen were here for a couple weeks to help us jam on the Hymenoptera Anatomy Ontology. We got some incredible feedback and will be talking about this work at the International Congress of Hymenopterists in Kőszeg, Hungary this June (at least seven Insect Museum people will be attending!) Thankfully, Lars made it safely back to Copenhagen despite Eyjafjallajökull’s best efforts…
  • We finished databasing our bumble bees (Apidae: Bombus spp.) and have moved on to Coccinellidae, while we also mix in some Heteroptera. We’ll bounce between bees and ladybird beetles for the next couple months. Time for us to tackle the GBIF bureaucracy so that we can become a provider!
  • István Mikó is visiting the Canadian National Collection for a few weeks in order to finish an ongoing revision and to look for more Ceraphronoidea material we can borrow.
  • We’re continuing our massive shuffle of equipment and furniture in the Museum, optimizing the space for a blend of digitizational (I know, that’s not a word) activities – from GigaPan (check out the Fulgoroidea drawers; we’ll finish Hemiptera in May), to collecting event data entry, to type imaging, to barcoding and sorting.
  • Five of us will be attending the digitization meeting at NESCent, today through Friday. Here’s the original post about the last meeting. Time to synthesize community feedback and write up a formal plan.
  • John Ascher from the AMNH visited to help us curate our bees, especially T. H. Mitchell’s wonderful collection.
  • We’re running Malaise traps in the Sandhill region of North Carolina, as well as some familiar spots north of Durham. These traps get sorted on Wednesday evenings, over pizza (5:00-9:00pm). Everyone’s invited to join us! Send me an email if you’re interested. I’m drafting a post about the workflow, which we’re trying to standardize. It’d be great to get some feedback about our plan.
  • We initiated a departmental contest to revitalize the eight display cases that reside outside of our classrooms (see photo below), which (apparently) haven’t been updated since humans hiked through Beringia. At least two of these displays will highlight research we’re doing in the Museum. I can’t wait!

ugly old display

Posted in curation, expeditions, news, phyloinformatics | 1 Comment »

position available at the NCSU Insect Museum

Friday, April 23rd, 2010

Do you need a summer (and possibly longer) job? If you hang out on the NCSU campus you might see these employment fliers cropping up on various billboards this week. The Insect Museum needs a dedicated student, with interests in insects, scientific imaging, databasing, biodiversity informatics, information science, and/or public outreach, to help us achieve the goals outlined in our NSF BRC grant.

Questions can be sent to Andy Deans (ncsuinsects@gmail.com).

/AA/EOE. ADA Accommodations: Dr. Andrew R. Deans ncsuinsects@gmail.com 919-515-2833.// NC State welcomes all persons without regard to sexual orientation./

Posted in curation, phyloinformatics | No Comments »

national specimen digitization effort

Wednesday, March 3rd, 2010

Imagine if you were put in charge of a giant warehouse full of money, and you had to devise a plan to earmark and distribute the funds in such a way that enables the digitization of ALL (or very nearly all) specimens in natural history collections in the USA:

collection in USA

What would that plan look like? Well, Brian Wiegmann and I were invited last month to a meeting at NESCent (Brian co-organized the meeting), where our charge was exactly that: devise a large-scale, national plan to digitize natural history collections over a 10-year period. The money doesn’t exist yet (nor do we know how much is required or how much we’ll get as a community), but the need for these data is very real.

The first summary of the plan is now out for comments, and there is an active campaign to rally the collections communities behind the idea. Feedback can be provided as a group email to the original participants (wg-digitization – AT – nescent.org), as individual emails to one or more participants listed on the meeting website, or as comments on the blog post summary.

What would your strategy be? Which components of the specimen digitization process should be prioritized – technology, data standards, crowd-sourcing, imaging, labor force, technology transfer, training, or _____? How would you involve federal agencies and international organizations? Note that the new program likely will not fund infrastructure (new cabinets, etc.), nor will it fund the collection of new specimens.

It’ll be fun to hear input from experts with diverse approaches and different issues (botanists vs. entomologists, database specialists vs. ecologists). As the director of an active natural history collection engaged in specimen-level databasing I’m very excited that this initiative is being pushed. We’re anxious for your input!

Posted in curation, insects, phyloinformatics | 1 Comment »

research computing associate position available

Tuesday, February 16th, 2010

We’re looking for a research computing associate! Details:

The Hymenoptera Anatomy Ontology project (HAO) at North Carolina State University seeks an innovative and creative programmer to help build a foundational resource for a broad range of disciplines, including biodiversity research, systematics, genomics, and evolutionary biology. The programmer will work with a small but dynamic team of researchers to develop the informatics infrastructure for the HAO. All HAO products will be open source and we encourage active involvement in open source based communities.

As a vertex of North Carolina’s Research Triangle NCSU benefits from close proximity to a large community of programmers and biologists, including the communities at NCSU’s Centennial Campus, Duke University, and the University of North Carolina at Chapel Hill, as well as our affiliation with the National Evolutionary Synthesis Center (NESCent).

The position is available from April 1, 2010 (negotiable) and is offered for one year, with the possibility of reappointment for a second year.

Required experience:

Candidates should have a 4-year degree in Computer Science or related field, plus 2 years full time programming experience OR a graduate degree that required significant programming and was in the field of evolutionary (including genomic) or systematic biology, philosophy, math, computer science, physics, or related field. Other requirements include:

  • demonstrated experience in web-based API development
  • intimate familiarity with XML and structured data
  • some experience with ontologies or semantic-web technologies (e.g., OWL)
  • excellent written and oral communication skills
  • ability to work with a team of people with diverse backgrounds

Desirable experience (in order of preference):

  • intimate knowledge or development of the TDWG standards and/or familiarity with the field of biodiversity informatics
  • extensive programming experience with Ruby and Java
  • formal education in philosophy or logic
  • experience developing browser or web-page plugins or portable applications
  • experience with social network integration, particularly as it applies to research related questions (e.g., Mechanical Turk and other crowdsourcing approaches)
  • experience in morphological evolution, developmental genetics or other fields of evolutionary biology
  • experience with visualization and manipulation of large datasets
  • previous contributions to open source projects
  • remote server management or systems administration

This is a 1-year time-limited position, with the possibility to reappoint for another year.

To Apply

Applicants should submit a cover letter, a one-page statement of interest, and a CV with at least two references. Clearly highlight or link to your past or current programming contributions. Creative applications are a plus – e.g., surprise us with a useful patch or a code audit of our existing software. Review of applicants commences March 15th and continues until the position is filled.

HR contact information (for questions about applying): http://www7.acs.ncsu.edu/hr/job_applicants/

Click on “apply here” then “search vacancies”. Search for position #101506

PI contact information (for questions about the project ONLY):
Andrew R. Deans
Department of Entomology
North Carolina State University
Campus Box 7613
2301 Gardner Hall
Raleigh, NC USA 27695-7613
email: andy_deans – AT – ncsu.edu

More information:
http://ncsu.edu/
http://hymao.org/
http://deanslab.org/
http://insectmuseum.org/
http://entomology.ncsu.edu/

//AA/EOE. ADA Accommodations: Dr. Andrew R. Deans andy_deans AT ncsu.edu 919-515-2833. NC State welcomes all persons without regard to sexual orientation.//

Posted in news, phyloinformatics | No Comments »

resolutions for 2010

Wednesday, December 30th, 2009

Ok, so we didn’t quite meet those resolutions for 2009. What are our resolutions for 2010?

  1. Take care of the humidity issue. Persistent monitoring and reporting are key to resolving this potential problem. We’ll also look into dehumidifying strategies – e.g., remove fan vents, install some dehumidifiers – before spring hits in 2010. This should be an easy problem to solve.
  2. Post regular pest monitoring results to our calendar. A follow-up on last year’s resolution. No excuses this year, we’ll get it done.
  3. Database the Coccinellidae and Aphidae. We have the tools and student-power we need, and this one of the tasks outlined in our BRC proposal. No sweat.
  4. Write North Carolina insect-of-the-week (yes, weekly!) blog posts. OK, this resolution is ambitious. We will cover one North Carolina insect species per week by posting information on its natural history, what our research collection holds for that taxon, how to find and preserve specimens, and, of course, photos of what these insects look like. I’d also love to offer a KML file of our NCSU specimens (you could view them in Google Earth!), alongside each post, but I bet we won’t be able to do that for all species. We’ve lined up a series of these blog posts already (check this blog on Friday mornings), thanks to the hard work of my ENT 502 students from last semester. This will definitely be fun!
  5. Profile the entire collection. We’ll follow McGinley’s (1989) classic profiling methodology or use the modified INHS system, but somehow, some way we will have the collection profiled in 2010 – the earlier the better. We’ll also post the results in a very public way, similar to this page by the Natural History Museum at the University of Oslo.
  6. No more legacy data. All new data will be captured electronically from the very beginning (in the lot stage), and all prepared specimens will get unique IDs. We’ll know – in real time – how many specimens we’re adding, rather than having to go back and count them at the end of the year.
  7. Establish a consistent weekly sorting/pinning/labeling session. We tried desperately last semester to meet weekly, but our schedules were never quite in sync. I’m confident that we can find our rhythm this year, though, and that we will finally process the ever-growing collection of bulk samples in our freezer. Which leads us again to our final resolution…
  8. Add 5,000 Hymenoptera specimens to the research collection. Either from bulk (mounted and sorted at least to family) or from unsorted pinned material (in which case specimens will be determined at least to genus).

I think those are reasonable and certainly laudable resolutions for 2010. We would definitely appreciate any input you might have regarding these efforts, and we wish you all the very best in the new year!

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Posted in curation, news, phyloinformatics | 1 Comment »

that time of year again

Thursday, January 15th, 2009

Time to evaluate and top off the ethanol in our wet collection (check!) and to renew our institutional memberships (double check!). Our membership in the Biodiversity Information Standards group (TDWG) is now current, as is our membership in the Society for the Preservation of Natural History Collections (SPNHC). NCSU's College of Agriculture and Life Sciences covers our membership in the Natural Science Collections Alliance, and our CITES registration doesn't expire until 2012, so I think we're good to go for the next 12 months.

Catching up on our memberships reminded me to review (again, but this time for realz) TDWG's Natural Collections Descriptions (NCD) data standard. It's been out for awhile, but I haven't taken a serious look until now. I don't profess to be an data standards expert, but I have a keen awareness of why they exist. The NCD looks pretty straight forward, and here's what I think it'd look like for the Insect Museum (* fields are required):

Header

*Author: Andy Deans
*Record Created Date: 2009-01-15 [What's the standard date format? Dublin Core points to W3C's date and time formats]

Collection

Collection Identifier: urn:lsid:biocol.org:col:1024 [I guess this could also be 'http://insectmuseum.org/'?]
Acronym or Coden: NCSU [This is from the old Arnett list, but I am not sure how to "indicate the source"]
*Collection Name: North Carolina State University Insect Museum
Associated Person(s): Andy Deans, Bob Blinn
*Description: ["main description...suitable for a general audience" - note to self: write something up]
Extent: Approximately 1.4 million specimens classified in Insecta and Chelicerata
Collection Type: Museum [defined by TDWG as "An institution for the procurement, preservation, study and exhibition of specimens and objects of value."]
Common Name Coverage: insects and other terrestrial arthropods
Conservation Status: [note to self: revisit McGinley's collection profiling strategy and see about applying it to our research collection]
Development Status: Active growth [!]
Formation Period: 1890-present
Kingdom Coverage: Animalia
Known to Contain Types: True
Living Time Period: Holocene [or Subatlantic?]
Physical Location: http://www.ncsu.edu
Primary Grouping Principle: Taxonomic
Primary Purpose: Research [but also Voucher and Education; can I add more than one?]
Related Material: [maybe our haiku contest should go here!]
Related Collection: [probably need to list here the collections we absorbed, e.g., the NCDA reference collection and others]
Specimen Preservation Method: Pinned [but also Fluid preserved, Slide mount, Cryopreserved, Glycerin, SEM stub; can I add more than one? I think so...]
Taxon Coverage: Arthropoda
Temporal Coverage: 1890-present
Access Conditions: http://insectmuseum.org/policies.php
Usage Conditions: http://insectmuseum.org/policies.php
IPR Statements: [note to self: think more about a statement on intellectual property rights]

Institution

Institution Identifier: http://www.ncsu.edu/
Name: North Carolina State University
Unit Name: Department of Entomology
Contact: http://entomology.ncsu.edu/
Type: University

Contact Details

Name: Andrew R. Deans
Family Name: Deans
Given Name: Andrew
Job Title: assistant professor
Role: director
Institution Name: North Carolina State University
Institution Unit: Department of Entomology
Post Office Box: 7613
Local Area name: Raleigh (I guess?)
Regional Name: North Carolina (I guess?)
Postcode or ZIP code: 20695-7613
Country Name: United States of America
Telephone Number: +1-919-515-3595
Fax Number: +1-919-515-7746
Email Address: andy_deans@ncsu.edu
URL: http://insectmuseum.org/
Logo URL: [we should probably design a logo!]

That's my first attempt, and the exercise got me thinking about a few things – how we should describe ourselves, why we need to profile our collections, and whether we need a formal policy on intellectual property rights. I'm sure the University covers that last one, but I must confess that I haven't read the policy. All in all I don't think I have any criticisms of this standard in its current state. I'll have to see what the hard core standards gurus have to say…

Posted in curation, phyloinformatics | No Comments »

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