News and Updates




Data Carpentry Workshop: a iDigBio and TTD-TCN Collaboration

posted Nov 11, 2014, 11:31 AM by Katja Seltmann

(This is a reposting from the iDigBio Blog, November 2014)

Data Carpentry - Please can we have some more?!

iDigBio and the American Museum of Natural History (AMNH) co-hosted a Data Carpentry Workshop on Monday and Tuesday, September 29 – 30, 2014.

What skills do researchers in the life sciences need to be equipped with today to address current issues facing our planet? How can they make best use of all the data available to them, now, and in the future?

To start off our Data Carpentry Workshop, University of Florida (UF) Botany Professor and iDigBio PI, Pam Soltis, shared her vision and historical perspective on the skills researchers need to make best use of data, now and going forward. From her own thorough grounding in statistical methods, Pam highlighted how changes in science, and data, necessitate the researcher’s need for new skills in her talk: Linking Heterogeneous Data in Biodiversity Studies: the need for data carpentry.

For two intensive, information-filled days of hands-on learning designed for beginners, 31 students tackled improving their spreadsheet skills, learned about the power of Open Refineto clean data and reveal data patterns via facets and clustering algorithms, discovered the power of the shell, found out just how simple it can be, to get a dataset from a spreadsheet into a database to make use of structured query language (SQL), and got an introduction to Rfor data analysis and visualization.

Broadening Participation.

Graduate students made up 60% of the participants, the other 40% were university faculty and staff. Nine students participated via Adobe Connect from the AMNH, including students from the City College of New York (CUNY), AMNH - Columbia University, and Hunter College. Three Information Science students from Florida State University (FSU) joined the UF students, faculty, and staff to make 31 participants total. Across diverse fields, there is a demand for beginner-level courses introducing researchers to up-to-date computational literacy, data literacy, and data management skills. Disciplines of participants ranged across Physics, Earth Sciences, Ecology, Zoology, Epidemiology, Botany, Genetics, Engineering, Social Science, Humanities, Tech Support, Public Health, and Information Science.

The Workshop Experience.

All available workshop slots at UF and AMNH filled in just 3 days, with four people left on the wait-list at UF. With a student-teacher ratio of 3:1, everyone found someone nearby, ready and willing to assist, if they ran into tricky bits.

The iDigBio Data Carpentry Workshop Wiki reveals all materials used and topics covered, and includes recordings, notes taken, links to the datasets and materials on GitHub, the participant list, and more. Using Adobe Connect (AC) software and Kevin Love’s know-how, UF and AMNH students met each other virtually to learn together and share problem-solving strategies. We took notes together using a MoPad, with help from our remote assistant fromUSGS-BISON, Derek Masaki. Thanks Derek! Scenes from the workshop are up on the iDigBio Facebook pages.

Tracy K Teal, Professor at Michigan State University (MSU) in Microbiology and Molecular Genetics, walked us through better spreadsheet skills and the power of the shell. Deb Paul (that’s me), highlighted the importance of quality data and showed how one tool, Open Refine, can be part of your scientific workflow to enhance your data and its fitness-for-use. Matt Collins (iDigBio Systems Administrator) provided a hands-on step-by-step introduction for us to the world of relational databases and SQL. All of these skills lead up to an interactive introduction to the scripting language, R, taught by Francois Michonneau, PhD candidate (Marine Invertebrates) at UF. Katja Seltmann, Entomologist and Project Manager for the Tri-Trophic Thematic Collection Network (TTD-TCN), provided instruction in the remote location – AMNH. In addition to our 5 instructors, we also had assistants to make sure no one gets too lost, or waits too long for help. The workshop depends on assistants to run smoothly. Part of the process of becoming a Data Carpentry instructor requires attending a Data Carpentry workshop, and assisting at one. Several of our assistants are in the process of becoming Data Carpentry certified.

AMNH students report they can’t wait to do this again. All at UF and AMNH are clamoring for more R, eager to pick up where we left off on day two, just as Francois got to the good stuff (in R) with his amazing demonstration of the power of all these skills combined. We’re thinking that Data Carpentry courses, normally two days, need a third day.

A bit on Assessment (more on this in a future post).

For assessment, Data Carpentry courses use not only pre and post workshop surveys, but also minute cards. Periodically, after a course module, students are asked to write down one thing they learned, and one thing they still find confusing. This immediate feedback provides mid-course correction opportunities, as well as valuable input for next courses. Some examples of minute card comments from our Data Carpentry workshop…

Something I learned

Something I still find confusing

Be careful with naming files, don’t use spaces

I have my own versioning schema. Are there standards for versioning?

Export spreadsheet data as CSV, or perhaps TSV

I’m still a bit confused about when to use () and [] in the same line

Basic R syntax

What are the benefits of using R as opposed to SPSS? <excluding cost>

Never understood cbind() before [now I do]

Still confused on some terminology – objects vs. variables? Vectors vs. factors?

Our post-workshop survey resulted in an overall workshop grade of A- and many comments indicating the desire for more such focused, hands-on training, targeted at beginners – and designed with the biodiversity researcher in mind. What are some lessons learned at this workshop? Our remote participant strategy seems to have worked well to extend the reach of our workshop beyond UF. Keys to making a remote workshop site (AMNH) successful include having an:

  1. on-site instructor in the remote location who is familiar with all the course materials and the skills being taught
    1. in the event the connection is lost, the remote instructor can carry on with the lessons
  2. instructor, or other individual in the remote location who can troubleshoot the audio / video issues that arise.

What’s Next?

  • Would you like to request a Data Carpentry Workshop? Please send an email toadmin@datacarpentry.org
  • Are you interested in becoming a Data Carpentry Instructor? We use the Software Carpentry training course to certify our instructors. Our goal is to cease to be needed because all scientists have the skills they need to manipulate their data. Until then, if you’ve got skills, want to enhance your skills, and the skill set of your colleagues in the biological and paleontological sciences community, please join us.
  • Discussions are just beginning for another Data Carpentry Workshop to be held at FSU in the Spring of 2015 with a remote location to be decided.
  • Note the broader community, across the planet, is converging on ways to define the skills that are needed and the best way to meet the demand for these skills. This includes conversations about how to get these skills into undergraduate and K-12 education so that incoming graduate students have them at the start of their advanced degree programs. For examples of this international convergence, see the upcoming Biodiversity Information Standards (TDWG) 2014 Interest Group / Task Group Meeting: Biodiversity Informatics Curriculum / Teaching and Workshop: Effective Biodiversity Data Management Trainingdescriptions!

Please let us know your thoughts. What skills do you need? What else do we need to cover? Got an idea for where to host one of these?

Thanks for reading and stay tuned for more Data Carpentry!


If you've made it this far, you might be wondering...

Just where did Data Carpentry come from?

From the COLLAB-IT meeting in September of 2013, one break-out group coalesced an idea into action to form Data Carpentry. The IT groups from NESCentBEACONiDigBioNEON,iPlantSESYNCDataONE, and NIMBios shared their observations about data literacy and computational literacy skills needs across the stakeholders in these overlapping communities. Course content needed to address these skills gaps make up the Data Carpentry curriculum.

Following the Software Carpentry model, Data Carpentry seeks to improve and enhance researchers skills needed to collect, manage, and analyze data efficiently. We aim to teach skills that result in reproducible, sustainable scientific workflows that result in discoverable, re-useable datasets and reproducible analysis.

Idigbio Collections for the 21st Century Symposium

posted May 5, 2014, 6:53 AM by Katja Seltmann   [ updated May 5, 2014, 6:54 AM ]

This is a reposting of the iDigBio website. You can attend remotely! 


On May 5-6, 2014, iDigBio, in conjunction with the NSC Alliance, will present a symposium themed 'Collections for the 21st Century'. The symposium will emphasize the value of collections data in meeting challenges facing biodiversity and human societies. Digitization of Bio-Specimens has brought a tremendous amount of data on-line for new and exciting uses in research and education. But we as scientists need to take the initiative and demonstrate ways in which the data is being used now, so that policy makers and administrators will provide ongoing support. Digitized data are valuable only if it is widely known as useful.

The symposium will demonstrate the value of biodiversity, and our natural history collections, to policy makers, administrators and others who use collections data and impact the levels of support for collections. The symposium will feature a full day of talks on May 5 and a half-day of talks on May 6. A workshop or other activities yet to be determined will be held on the afternoon of May 6. Topics of discussion will include uses of taxonomic, spatial, and temporal data on biodiversity to address big-science questions related to human health, climate change, food security, and related issues, as well as more fundamental investigations related to understanding and protecting biodiversity. We will keep those who register informed of our plans as they develop. Attendance will be limited to 80 persons.

Registration for the symposium is free, but all travel-related expenses (e.g., airfare, hotel, meals, ground transport) are the responsibility of each participant.  Information on accommodations at a discounted rate will be provided once you register.

Register for this Symposium

Workshop Wiki: https://www.idigbio.org/wiki/index.php/Collections_for_the_21st_Century

Agenda: https://www.idigbio.org/sites/default/files/workshop-presentations/collections21century/Collections_for_the_21st_Century_agenda.4.28.pdf

Remote participation will be available via Adobe Connect: http://idigbio.adobeconnect.com/e540omdlz94/event/event_info.html

 

Start Date: 
Monday, May 5, 2014 (All day) to Tuesday, May 6, 2014 (All day)
Location: 
University of Florida
City: 
Gainesville
State: 
Florida

Female Entomologist: Patricia Vaurie (1909 - 1982)

posted Apr 3, 2014, 11:17 AM by Becky Fisher

Patricia Vaurie and her husband were both enthusiastic about natural history. Patricia has an extremely successful career studying beetles while her husband pursued his artistic interest in North American birds. Their trips together provided the AMNH Entomology collection with a breadth of data that is still productive and informative to the field as we continue to digitize her plant bug specimens. 

Patricia Wilson was born on September 14, 1909 in Swarthmore, Pennsylvania. While she was still young, her family moved to New York City. By 1920, they lived only a block away from the American Museum of Natural History. Patricia attended high school and later Barnard College, Columbia University. She graduated in 1931 with a degree in English literature.

During World War II she started volunteering as a technical assistant in the Department of Insects and Spiders (now the Department of Invertebrate Zoology). Around this time she met her husband Charles Vaurie. He was a dentist in New York with an avid interest in painting North American birds. Although Patricia focused on the study of beetles, the two of them appreciated their mutual interests in natural history. They were married in 1934.

By 1947 she achieved the title of Assistant and by 1957 became a Research Associate. Patricia published 77 revisionary studies of beetles throughout the course of her work. She received a total of four grants from the National Science Foundation to study Diplotaxis (Scarabaeidae) and Metamasius (Curculionidae). According to her glowing obituary, her colleagues held her in high regard for her meticulous and usable work.



The TTD-TCN project digitizers at the American Museum of Natural History are still benefitting from her enthusiasm for insects and detail. Although Patricia specialized in beetles, she collected a variety of other insects while on trips for the Natural History Museum with her husband. Interestingly, the Specimen Database tells us that most of their work trips took place during the months of July and August in pleasant locations such as the Bahamas, Cuba, New Mexico, Guatemala, the Ruins at Palenque (dark blue peg), and Flagstaff, Arizona. This sounds like an extremely convenient way to skip out on New York City summers. Moreover, these trips were often funded as expeditions. The map to the right represents all of the localities that the Vauries collected plant bug specimens during the D. Rockefeller Mexico Expedition of 1953 (green pegs).

We have been digitizing many species that were collected by her but were later determined by other AMNH entomologists. This tells us that she collected for the greater good of the field even though beetles were clearly her specialty. The current, massive plant bug collection at AMNH does not solely exist because of previous plant bug enthusiasts. Although such specialists have left a huge impact, the enormity of the project is just as dependent on the previous work of enthusiastic entomologists in general.

Although some of these plant bugs were collected without a clear objective, the usefulness of these insects has only increased over time. Take the image of the Josephinus reinhardi (light blue star) for example, it was collected is 1952 by Patricia Vaurie and it sat until 2005 when M. D. Schwartz determined the specimen. Now, in 2014, it is available for digitization and has become a small piece of data in a growing database.

 

 

References and Suggested Further Reading:

Herman, Lee H. "Patricia Vaurie: 1909-1982." The Coleopterists Bulletin 36.2 (1982): 453-57. JSTOR. Web. 01 Apr. 2014.
        <http://www.jstor.org/stable/10.2307/4008093?ref=search-gateway:548613e1e2149ee32ffd8dc31218ceca>.

Ratcliffe, Brett. "PATRICIA VAURIE." PATRICIA VAURIE. University of Nebraska-Lincoln State Museum - Division of Entomology, 01 Jan. 1988. Web. 01 Apr. 2014.
        <http://museum.unl.edu/research/entomology/workers/PVaurie.htm>. 

Short, Lester L. "In Memoriam: Charles Vaurie." The Auk 93.3 (1976): 620-25. JSTOR. Web. 01 Apr. 2014.
        <http://www.jstor.org/stable/10.2307/4084962?ref=search-gateway:7d6818bef46661b9ca5037987711093e>. 

Maps built using google.maps.com and the Tri-Tropic Specimen Database.

Photo of Patricia Vaurie from her obituary in The Coleopterists Bulletin

 

Article by Becky Fisher: TTTCN Intern and Masters candidate at Columbia University in Museum Anthropology.

Female Entomologist: Grace Olive Wiley (1883 - 1948)

posted Mar 13, 2014, 11:38 AM by Becky Fisher   [ updated Apr 3, 2014, 9:00 AM ]

Grace Olive Wiley is most widely known for her illustrious career as a fearless and controversial snake collector. She frightened and informed her audiences by demonstrating nurturing relationships with her snakes. Snakes and insects have been associated with negative images of hypnotizing demons or filthy infestations. Her closeness with snakes captures attention, to say the least, but I think it also overshadowed her contributions to the field of entomology. This article is an attempt to shed some light on her life, her specimens in the Tri-Trophic TCN project and the field of entomology before she immersed herself in a world of herpetology exhibitionism.

Grace Olive Wiley was born and raised in Chanute, Kansas in 1883 on a farm. She attended the University of Kansas and achieved a bachelor degree in Entomology. She worked as an entomologist at the University at a time when women struggled to gain acceptance in scientific fields. The University of Kansas was unique. By 1867 they had already appointed their first (as well as one of the country's first) female professor, Cynthia A. Smith. In 1922, the Kansas University Science Bulletin put out Wiley's Life History Notes on Two Species of Saldidae (Hemiptera) Found in Kansas. Her enthusiasm in the field was also recognized by her male academic advisors in Kansas. Her professor H. B. Hungerford wrote in The Life History of The Toad Bug, "The live insects supplied by Mrs. Wiley [from her home in Chanute] thus made possible the notes here reported, and I wish to acknowledge my gratitude to her for her kindness".

By 1923, Wiley became the curator of the Minneapolis Public Library’s natural history museum. Although it is now defunct, this position made her one of the first female zoo curators in the world. This was also the year she announced her discovery of a new species of Rheumatobates from Texas in The Canadian Entomologist. She donated her private collection of reptiles which included 150 species and 330 individuals to the zoo and her reputation as a reptile expert took off. She quickly became the first person (man or woman) to successfully breed rattlesnakes in captivity. 

She believed that deadly snakes could be tamed and she refused to use hooks or other safety devices to handle them. Instead, she would gently stroke them and speak to them (snakes are deaf). Her unorthodox methods caused friction within the Zoo’s administrators. They demanded that she stop handling the snakes even though they were her own collection. Although she was never bitten at the Zoo, she was gavin a choice to either use safety equipment or leave. Wiley left, took her snakes with her and started a new job at the Brookfield Zoo outside of ChicagoThis new zoo wanted to display reptiles in a more natural setting. Their displays replicated the snakes' natural habitats and were big enough to hold multiple snakes at once. Before then, it is was customary to keep reptiles in separate metal cages without any stimulation. Yet again, Wiley’s habits of leaving the reptiles’ cases open caused problems between herself and the Director. She was fired after 19 venomous snakes escaped. 

Again, she packed up and moved. This time to Long Beach, California where she established a roadside zoo relatively close to L. A. Her snakes were featured in a few of the sensational movies of the time such as The Jungle Book, Trade Wind and Cobra Woman. During filming she was always on set and appeared onscreen as a snake charmer in the 1940 film Moon Over Burma. She charged 25 cents to join her, wander her roadside property and handle the snakes. She moved twice because neighbors complained. She had been bitten many times and lost two fingers to her Komodo Dragon.

On July 20, 1948 the renowned freelance journalist Daniel Mannix was visiting her zoo to finish an interview and take some photos. While posing with one of her new Indian Cobras, it bit her on her middle finger. Cobras have short fangs and need to chew on their prey to transfer their venom. Unfortunately, the cobra was able to chew on her finger for 30 seconds before Wiley was able to remove it. She was 64 years old. She calmly put the snake back in its cage and told the journalist to get her snakebite kit. Sadly, the kit was about 20 years old, the syringes were corroded and the serums were broken or evaporated. Wiley fell into a coma, was placed in an ambulance and died 65 minutes later at Long Beach Municipal Hospital. The hospital only carried anti-venom serums for North American snakes.

Before her unexpected death, Wiley had planned to sell her reptile collection to the Griffith Park Zoo. However, her estate was not able to find a buyer. As a result, her exotic collection was auctioned off bit by bit to the highest bidders. Overall, it was worth $3,000. The Indian Cobra that fatally bit Wiley was purchased by a man who displayed it as the “Lady-Killing Cobra” at a tourist spot in Arizona.

Wiley’s career as an entomologist was relatively short but productive. So much of it can be overpowered by her mystical, dangerous and high-profile herpetology career. Yet, we are still reaping the benefits of her work in entomology today. The green pegs on the map represent the various locations from which plant bugs were collected by Grace Olive Wiley. These specimens are located in the AMNH collection, the United States National Museum of Natural History, the University of Massachusetts Museum, the Oregon State Arthropod Collection, the University of Minnesota at St. Paul and the University of Kansas.


References and Suggested Further Reading:

http://www.czs.org/czs/About-CZS/History/Grace-Olive-Wiley

http://www.dkulczyk.com/tag/grace-olive-wiley/

http://ljnoddingherpetology.wordpress.com/2014/01/16/grace-olive-wiley-the-snake-whisperer/

http://kuscholarworks.ku.edu/dspace/bitstream/1808/5067/1/MARSV15N2A7.pdf 

Maps built using google.maps.com and the Specimen Database

Photo of G. O. Wiley from http://www.chicagoherp.org/bulletin/41(Supplement).pdf 


Article by Becky Fisher: TTTCN Intern and Masters candidate at Columbia University in Museum Anthropology.

Female Entomologist: Edith Marion Patch (1876 – 1954)

posted Feb 20, 2014, 1:33 PM by Becky Fisher   [ updated Mar 27, 2014, 10:38 AM ]

While digitizing specimens in the collection, we gloss over thousands of names of collectors worldwide. Although the main intention is to map and study the lives of the insects, we have wondered if we were also mapping the lives of the collectors. This series is an opportunity to use the digitized collection to map the lives of women who have contributed to the American Museum of Natural History collection and the Tri-Trophic TCN project. Who were they? What are their stories?

Like many entomologists at the time, Edith Marion Patch’s first recorded interest was butterflies. In her senior year of high school she wrote an essay about monarchs that won $25.00. With her prize money she purchased the Manual for the Study of Insects written by John Henry Comstock and illustrated by his wife, Anna Comstock. The Comstocks were entomologists at Cornell University whom Patch would later befriend. 

Edith Patch attended the University of Minnesota in 1897 and graduated in 1901 with a Bachelor in Science. Despite her qualifications, she couldn’t find a job in entomology so she took a position teaching English at a high school in Minnesota for two years. Finally, in 1903, she was invited by Dr. Charles D. Woods to organize a Department of Entomology in Orono, Maine. Today UCBs Department contains digitized plant bugs collected by E.M. Patch in Orono, Maine. Three specimens of Cryptomyzus (Cryptomonyzis) ribis and five of Eirosoma ulmi are currently in the database.

EM Patch 1916  - edithpatch.org

Initially, she wasn’t offered a salary and Dr. Woods was “ridiculed for appointing a woman in a man’s field” (http://www.edithpatch.org/). To earn a living wage, he arranged for Patch to teach English in the area while she organized the Entomology department. Within a year, Patch had proven herself to her male coworkers, established the department and earned herself a salaried position.

For her masters degree she attended the University of Maine in 1910. Although a few websites say that Patch earned her PhD from Columbia University, she actually attended Cornell University in 1911 for her doctorate. At Cornell she became colleagues with the Comstocks. 

In 1930, Patch became the first female president elected to the Entomology Society of America.She was ahead of her time in the early 1900s. It is said that she warned against the indiscriminate use of pesticides, such as DDT, forty years before Rachel Carson’s Silent Spring (1962) was published. She was concerned about the devastating impact pesticides would have on songbirds amongst other dangers. She was one of the original environmentalists and advocated for education of the natural world, especially for children. Despite her busy career in entomology, she also published books for children starring accurate, insect characters. She retired to her home in Orono, “Braeside," in 1937 as “Entomologist Emeritus” and lived there until she passed away in 1954.

Check out her children’s literature: Hexapod Stories, Bird Stories, Dame Bug and her Babies and Elm Leaf Curl and Wooly Apple Aphidhttp://amzn.to/1mf9OAc


References & Suggested Further Reading:

http://www.edithpatch.org/

http://www.rachelcarson.org/Biography.aspx#.Uv0giEJdUck

http://www.distinguishedwomen.com/biographies/patch-em.html

Article by Becky Fisher: TTTCN Intern and Masters candidate at Columbia University in Museum Anthropology.

Crowd Sourcing The New York Botanical Garden Herbarium Plant Database

posted Sep 12, 2013, 10:51 AM by Katja Seltmann   [ updated May 5, 2014, 6:52 AM ]

This is a reposting of the NYBG Plant Talk


Michael Bevans is the Information Manager for Digitization at The New York Botanical Garden Herbarium.


Virtual Herbarium ImageThe William and Linda Steere Herbarium at The New York Botanical Garden houses over 7 million plant specimens gathered from around the world over the course of 250 years.

Plants supply most of the world’s food, fuel, shelter and medicine, and plant specimens help us answer the most critical questions facing our planet. How many species are there and how are they related? What environmental factors control their growth? And how do plants respond to climate change? Now you can help scientists to better understand our planet by transcribing plant specimen labels in our newly released crowd sourcing effort, hosted by the Atlas of Living Australia.

Choose an expedition studying the Oaks of North America or the Plants of the Caribbean. Click the “Start Transcribing” button to log in and get started.

To learn more about the William and Lynda Steere Herbarium, make sure to watch “Treasures of New York: The New York Botanical Garden” this Thursday, June 27th at 10:30pm on Channel Thirteen.


Short Course on Biological Specimen Informatics

posted Aug 15, 2013, 1:05 PM by Katja Seltmann   [ updated Aug 15, 2013, 2:29 PM ]

The Tri-Tropic Database Thematic Collection Network recently finished up an exciting course about present best practices for specimen-level data management. The two-week Short Course on Biological Specimen Informatics (Specimen Short Course; syllabus and more information: tcn.amnh.org/home/specimen-course) was designed as a first introduction to biological informatics with early career graduates students in mind. The Specimen Short Course gathered individuals from 18 different institutions across the United States at the Richard Gilder Graduate School (American Museum of Natural History  - rggs.amnh.org) in order to specifically address research specimen data capture issues through training, from the field to preserved collections. Instructors for the course were staff were Mike Bevins (Information Manager, NYBG), Christine Johnson (TTD co-PI, AMNH), Rob Naczi (TTD  PI, NYBG), Randall Schuh (TTD PI, AMNH), Katja Seltmann (TTD Project Manager, AMNH), Steve Thurston (Image Specialist, AMNH), Melissa Tulig (TTD co-PI, NYBG), and Kim Watson (TTD Project Manager, NYBG).

Unarguably, biological research generates a great deal of specimen level data. These data can be complex and include familiar collection level data (the focus of many broad museum digitization efforts) as well as highly specific data depending on the research question/s. Researchers have the additional need of high accessibility to all of their data, either through bulk download, or by direct database access, in order to perform analysis. The results of early training for students is mutually beneficial, as improved specimen handling techniques facilitates research, and well-managed data according to community standards allows for greater dissemination of the end products. In order to create a workflow that fits their research needs, participants in the Short Course learned about, and worked on, projects with several tools including: Arthropod Easy Capture (sourceforge.net/projects/arthropodeasy), Specify (specifysoftware.org), ScratchPads (scratchpads.eu), SimpleMappr (simplemappr.net) and others. At the same time students gained valuable expertise mapping datasets to DarwinCore, manipulating data with Open Refine (openrefine.org), Excel, and MySQL.

Enabling students to manage research was one aspect of the Specimen Short Course. The second was to place these efforts in the context of the larger biodiversity informatics community. The course involved visiting research areas at the American Museum of Natural History and the New York Botanical Garden, allowing participants to gain a sense of what the various workflows at these institutions are like, as well as the collection requirements for vouchering specimens at the end of a research project. These experiences helped participants develop techniques and collecting protocols that they could use in their own research.

Imaging was another important component discussed as a means of data capture. At the New York Botanical Garden, participants in the course got hands-on experience photographing plant specimens. At AMNH, insect specimens were the focus. Participants got to see how high-quality images of small insects are taken, and visited the museum’s imaging lab to learn about the technology at work there.  They also learned about how images could be incorporated into their databases to strengthen specimen records.

            As the course progressed participants began to plan how they will use databasing techniques and other resources discovered through the Specimen Short Course. Each participant brought some of his or her data to the course and began to develop a workflow that best matches their individual research needs. As a culmination of the course, each participant delivered a presentation on how they will continue to incorporate the techniques they had learned into their own research.

            By the end of the course, each participant had gained not only a better understanding of specimen informatics techniques, but also a sense of how they could apply these techniques to their own research. The goal of the course was to train students in present best practices for specimen-level data management from the field to preserved collections, and how a specimen management plan can facilitate addressing research questions. The experiences they gained through the course will aid them in producing and making available datasets that will be of great use to them and countless other researchers.


Authors: Jeremy Frank (Short Course Participant) & Katja Seltmann (TTD Project Manager, AMNH)

Staten Island Museum Prepares for 17-Year Cicada Emergence

posted Apr 4, 2013, 10:00 AM by Alexander Bolesta   [ updated Sep 12, 2013, 10:54 AM by Katja Seltmann ]

With the three 17-year species of Magicicada from Brood II emerging this year in the eastern United States, the Staten Island Museum, co-founded by cicada expert William T. Davis (1862 – 1945), is focusing on making the most of this infrequent event. Their current temporary exhibition, "They're Baaack! Return of the 17-year Cicadas," along with planned workshops and nature walks, will inform visitors about these unique bugs in the coming months. This event happens to coincide with the our digitization of the cicada collection at the Staten Island Museum, which includes many specimens from previous emergences of Brood II, as well as the other broods of the 13 and 17-year cicadas. Posts on the Staten Island Museum's Tumblr and Blogspot sites offer information about local ecology and news about the museum, including their relation to the TTD.

          Blogspot Article About TTD

            Image from Staten Island Museum Blogspot site

Post by Alexander Bolesta: Database Assistant at the American Museum of Natural History, and Curatorial Assistant at the Staten Island Museum

Collection Highlight: The Staten Island Museum

posted Nov 13, 2012, 7:37 AM by Alexander Bolesta   [ updated Sep 12, 2013, 10:55 AM by Katja Seltmann ]

One of the exciting aspects of the Tri-Trophic Database project is the cooperation that occurs between different institutions in the name of science. Each of the 30+ museums involved with the project offers a wealth of experience in addition to the diversity that comes from adding their collections to the database. Of these, the Staten Island Museum in New York City offers a cicada (family Cicadidae) collection of about 35,000 specimens: the second largest collection of cicadas in the world. Since cicadas belong to the order Hemiptera, this comprehensive collection is a perfect addition to the Tri-Trophic Database.

Staten Island Museum main entrance; downloaded from http://bit.ly/TXJnCz
             Staten Island Museum main entrance. Downloaded
                                from http://bit.ly/TXJnCz

Specimen collection room where the cicadas are housed at the Staten Island Museum. Photograph by Alexander Bolesta.
     Specimen collection room where the cicadas are housed at the
        Staten Island Museum. Photograph by Alexander Bolesta.



The Staten Island Museum, previously the Staten Island Institute of Arts & Sciences, and the Staten Island Association of Arts & Sciences, was founded in 1881 as the Natural Science Association of Staten Island by a group of 14 local naturalists who were concerned that overdevelopment would lead to the destruction of Staten Island’s natural history. By pooling their resources, these environmentalist pioneers were able to put together a collection worthy of drawing public attention, and, in 1908, the museum opened its doors. Associates of the museum have since kept a continuous record of the changing ecosystem and environment on Staten Island, while inspiring the creation of establishments including the Staten Island Zoo, Staten Island Historical Society, Staten Island Greenbelt, and the New York Botanical Garden. To this day, the Staten Island Museum carries out specimen acquisition and field work, in addition to special events like annual bird counts in conjunction with the Audubon Society.

Permanent natural history exhibit at the Staten Island Museum. Photograph by Alexander Bolesta.
         Permanent natural history collection at the Staten Island 
                 Museum. Photograph by Alexander Bolesta.

The Staten Island Museum has been amassing a collection of specimens from the areas of natural science, art, and history since the days of the founders, and now boasts a collection of over half of a million specimens and pieces of art. One of the founders, William Thompson Davis, took a particular interest in the insects known as cicadas. Born in 1862 in New Brighton, Staten Island, Davis played a big role in the development of the Natural Science Association of Staten Island and its derivatives, despite being, for the most part, self-taught. His sense of wonder resulting from his study of cicadas can be seen most succinctly in his choice of name for the genus of 13- and 17-year periodical cicadas: Magicicada.


William T. Davis in the field. Downloaded from http://bit.ly/Umikx3
William T. Davis in the field. Downloaded 
            from http://bit.ly/Umikx3

His efforts over half of a century resulted not only in the accumulation of the world’s second largest cicada collection, as noted above, but it led to him formally describing over half of the known species of cicada in North America. As a result, the Staten Island Museum’s cicada collection includes many of the type specimens that were used by Davis as the official examples of these species. During his career, Davis was published extensively in the Journal of the New York Entomological Society, and even held positions there as treasurer and as delegate to the New York Academy of Sciences. Davis passed away in 1945, leaving behind an impressive list of accomplishments. In 1955, the 51 acre New Springfield Bird Sanctuary that was created in 1933 thanks to efforts by Davis and the National Audubon Society was expanded to 260 acres and was renamed the William T. Davis Wildlife Refuge: a fitting dedication to one of New York City’s premier naturalists.

Sample from the William T. Davis Collection of Cicadas. Photograph by Alexander Bolesta.
          Sample from the William T. Davis Collection of Cicadas.
                        Photograph by Alexander Bolesta.

Resources:

Abbott, Mabel. The Life of William T. Davis. Ithaca: Cornell University Press, 1949. Print.

"Collections: Natural Science Collection." Staten Island Museum. N.p.. Web. 24 Oct 2012. <http://bit.ly/RV8kwn>.

Davis, William. Days afield on Staten Island. New York: L.H. Biglow & Co., 1892. Print. <http://bit.ly/TCLebD>.

Davis, William. North American cicadas. 1. New York: Society Quarterly, 1921. eBook. <http://bit.ly/UAqZC2>.

"Freshkills Park." Official New York City Web Site. N.p., n.d. Web. 24 Oct 2012. <http://bit.ly/X37UtG>.

"History." Staten Island Museum. N.p.. Web. 24 Oct 2012. <http://bit.ly/IFErwo>.

Journal of the New York Entomological Society. 30. New York: Society Quarterly, 1922. eBook. <http://bit.ly/TXFdL2>.

Journal of the New York Entomological Society. 31. New York: Society Quarterly, 1923. eBook. <http://bit.ly/TXFdL2>.

Pratt, Jr., George O., G. K. Schneider, and Mathilde P. Weingartner. "The William T. Davis Wildlife Refuge and its Environs." Proceedings of the Staten Island Institute of Arts and Sciences. 24.2 (1969): n. page. Print.

"Staten Island Museum." Wikipedia, The Free Encyclopedia. Wikimedia Foundation, Inc, 09 Oct 2012. Web. 24 Oct 2012. <http://bit.ly/TCLlUp>.

"William T. Davis." Wikipedia, The Free Encyclopedia. Wikimedia Foundation, Inc, 03 Feb 2012. Web. 24 Oct 2012. <http://bit.ly/SYVJcZ>.

Zelasnic, Laura. "Records of the Herbarium (RG 4) CHARLES ARTHUR HOLLICK RECORDS (1873-1979)." The New York Botanical Garden. N.p., n.d. Web. 24 Oct 2012. <http://bit.ly/TGApqY>.


Article by Alexander Bolesta: Database Assistant at the American Museum of Natural History, and Curatorial Assistant at the Staten Island Museum

Digitization Milestone at the University of Minnesota Herbarium

posted Oct 29, 2012, 11:40 AM by Katja Seltmann   [ updated Sep 12, 2013, 10:59 AM ]

Here at the University of Minnesota Herbarium (J.F. Bell Museum of Natural History), we have reached our first milestone – we have finished photographing our first plant family, the Pinaceae (almost 1200 specimens)!   

Anita F. Cholewa, Curator of the UM Herbarium (MIN) and Hannah Conley in front of their digitization light box and workstation.

The Pinaceae also will probably be our most difficult.  Since pines produce thickened bulky cones, these were often removed from the branches during the collecting stage to make filing in the museum more efficient, but it now meant cones had to be reunited with their branches, both barcoded, and both photographed.  Given the thickness of some cones, this was not always an easy task.


(Pinus lambertiana, sugar pine, branch and cone)

Additionally, spruces and hemlocks have a tendency to lose their needles upon drying, leaving specimens looking like winter collections of plant skeletons.   Thankfully most needles are captured during the drying stage and kept in small packets attached to the specimens, but the flip side required us to remove some of these needles so they could be photographed with the branch skeletons. 

(left: Tsuga canadensis, Canadian hemlock; right: Congdon collection of Pinus albicaulis, whitebark pine)

Although a difficult and time-consuming group of plants, the Pinaceae also included some interesting specimens.  Among our Minnesota plants was a collection of Tsuga canadensis (Canadian hemlock) that consisted of a cross-section through the trunk of the most northwestern and isolated population in the state.  And because our specimen database includes numerous collections from national parks and adjacent states these were also photographed.  These included historical collections by Joseph Whipple Congdon from Yosemite, among the earliest botanists collecting in that region.




Article by Anita F. Cholewa, Curator of the UM Herbarium (MIN)

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