Smithsonian Institution National Museum of Natural History

Biocuration & Cyberinfrastructure Development for Plant DNA Barcoding

Intern: Zhuo (Tony) Zhang

Code: NMNH-10

The DNA plant barcoding project is a multi-year effort aimed at applying DNA sequence data to flowering plant identification. DNA barcoding uses the information of one or a few gene regions to identify species of life and will serve as an important tool in plant taxonomy and biodiversity discovery. For this project two or three interns will work in a team or independently organizing labeling and recording project materials and data including tissue samples voucher specimens and geographic information according to taxonomic hierarchies and data protocols. The goals of the project are to connect DNA barcoding information from different sources to correct inconsistencies and errors in data representation and to help establish an infrastructure to maintain data consistency and accuracy. Applicants should be comfortable handling fragile botanical specimens and working in a lab environment.

Qualification: Working knowledge of MS Excel strong organizational skills and familiarity with botanical nomenclature required. Prior knowledge of DNA barcoding terminology useful but is not mandatory.

The World of Maps

Intern: Chutimon Sindhuprama

Code: NMNH-11

There are over 30 000 maps in various research Departments of the National Museum of Natural History dating from the 1860s to the present. A project has been underway to organize the maps create images of them and enter data about them into a database. Depending on the student's skills and interests s/he would assist in identifying obscure maps creating images of the maps editing the images entering information about the maps into the database and/or cleaning up the database code and web interface. The database is written in Microsoft Access and its primary user interface is in ColdFusion / HTML / SQL.

Qualification: Interest in maps and some knowledge of geography. Basic computer skills.

Labeling Parasitic Wasps American Chestnut Land Trust Hymenoptera Biodiversity Survey

Code: NMNH-01

Sampling for this project has been conducted since 2006 in numerous localities throughout the American Chestnut Land Trust in Calvert County Maryland. This is one of the last intact watersheds draining directly into the western side of Chesapeake Bay. It encompasses beach strand brackish and freshwater habitats. Our collection techniques employ malaise traps to passively sample insect populations and generate tens of thousands of specimens per year. The specimens have been mounted on pins but await labeling. This is a multi-agency endeavor involving the USDA's Systematic Entomology Lab the Smithsonian Institution's Department of Entomology and the Maryland Department of Natural Resources. Interested candidates would be trained in labeling techniques for prepared hymenopteran specimens.

Qualification: Interest in biological/entomological science and combined laboratory work preferred.

Labeling Parasitic Wasps from Color Preference Survey

Code: NMNH-02

Sampling for this project was conducted in May-June 2007 to determine color preference for various taxa of Hymenoptera (bees wasps parasitoids) based upon passive sampling with plastic bowl traps. Seven color treatments (red blue fluorescent blue fluorescent yellow yellow white and transparent) were tested across 16 transects sampled every other day for one month (3 360 samples). The specimens have been mounted on pins but await labeling. This is a multi-agency endeavor involving the USDA's Systematic Entomology Lab the Smithsonian Institution's Department of Entomology and the U.S. Geological Survey. Interns will be trained in labeling techniques for prepared hymenopteran specimens.

Qualification: Interest in biological/entomological science and combined laboratory work preferred.

Biodiversity Informatics: Studying Jellyfish Biogeography using Computer Modeling

Code: NMNH-03

We are seeking a motivated student to support our efforts in studying the biogeography of open ocean hydrozoan jellyfishes of the subclass Trachylina. In an effort to understand the geographic and depth distributions of these animals on a global scale we are adapting biogeographic modeling techniques developed for terrestrial ecology to suit our needs. In a nutshell computer algorithms are frequently used to relate species occurrence data to the environmental conditions found at the collection sites of organisms. The correlations between environment and species occurrence can then be used to derive predictions of potential distributions of suitable habitat and thus species. The crucial step for this type of research is gathering reliable occurrence data as input for the modeling algorithm. We seek a student to help us developing a local database that contains species occurrence data and associated information. This data will be gathered under our guidance from the scientific literature as well as labels in specimen jars in the Smithsonian's collections.

Qualification: Motivation to be involved in a research project in its developmental phase. Interested in researching the scientific literature and working with specimens. Working knowledge of Microsoft Excel required; familiarity with ESRI's ArcGIS desirable but not necessary.

Host-use biogeography of sponge-dwelling Synalpheus snapping shrimps

Code: NMNH-04

Synalpheus are a highly diverse group of snapping shrimps that reside in the canals of sponges living in coral reefs and have become a model system for understanding the origin and maintenance of biodiversity in tropical habitats. Museum scientists have recently completed an extensive survey of Synalpheus and the sponges they live in across several different sites in the Caribbean (Belize Panama Jamaica Curaçao and Barbados) and described and photographed several new Synalpheus species. The intern will assist with two specific aspects of this project. First in order to investigate how shrimps adapt to their host sponges the intern will assist in measuring sponge canals (using photographs of sponges taken in the field) and measuring shrimp collected from the sponges. Second the intern will help compile taxonomic information (including photographs drawings and ecological information) into a Power Point presentation and/or set of web pages for the Encyclopedia of Life and other taxonomic databases.

Qualification: Experience working with specimens (e.g. through an invertebrate zoology or other organismal biology class) and basic computer skills (especially working with images) are necessary. Experience setting up websites is a plus but not required.

Biographical History of Crustacean Research

Code: NMNH-05

The intern will: convert a collection of ~ 400 portraits biographies and associated references archived in our "Gallery of Carcinologists" to electronic format for subsequent web posting on the IZ website; scan portraits photographs negatives and biographical text using flat-bed auto-feed and/or book scanner for archival and permanent storage purposes; edit digital images using Adobe Photoshop photo-editing program; save images as TIFF files at high resolution (mostly 600 DPI); save text files as PDF files; arrange all files in an organized fashion in designated subdirectory on computer; files backed up daily; burn completed digital files onto CD/DVD for permanent storage; label and organize CD/DVD properly; cross-check portraits scanned with database listing and file folders; update database.

Qualification: Computer skills: file management and organization; burning files to CD/DVD; basics of image scanning; experience using scanning equipment; experience with Adobe Photoshop or any other photo-editing program; experience with MS Excel and/or MS Access files; independent worker.

Digitally Archiving Crustacea Publications

Code: NMNH-06

The intern will scan edit and convert to pdf files Crustacea publications (reprints or part of a bound volume or book). Many useful and important publications are often requested by colleagues and students; however some are in limited quantity or are in very poor condition. Converting these publications to PDF format will make them readily available to the requester.

Qualification: Neat and organized; independent worker; skilled/experienced in scanning documents using a flat-bed scanner or self-feeding scanner; editing files (as needed in photo-editing program; e.g. Adobe Photoshop); converting scanned files into PDF files in archival format; skilled in computer file management; skilled in burning computer files onto CD.

Assessing Meaningful On-Line Participation for the Ocean Portal

Code: NMNH-07

In September 2008 NMNH opened the Sant Ocean Hall – the museum's largest permanent exhibit and one that has been well received by the public. In September 2009 the museum expects to launch the companion Ocean Portal – an online destination to inspire ocean literacy. Targeting “tweens” 8-13 year olds middle-school teachers and young adults 18-34 year olds a high level of online participation is expected. In February the portal will just be starting to be built using Drupal an open–source content management system. The portal is expected to have extensive links to social media such as Facebook Twitter Digg etc. There are clear educational goals of the Ocean Portal. The intern will read the Portal Business Plan to absorb the educational goals and think how and which social media sites would best enhance learning and further how could we assess the learning that has occurred particularly whether participation in the social media is a valid measure of learning or connectedness. The outcome of this project can be alternatively written or presented to the portal team.

Qualification: This opportunity is best suited for candidates with experience thinking through the “why” of online interactions. This requires extensive familiarity with websites web 2.0 tools and social media. Experience with or understanding of some of the current web statistical tools such as WebTrends or Google Analytics would be a big plus. The candidate will be expected to work independently with minimal supervision.

Seamlessly Navigating the Web

Code: NMNH-08

In September 2008 NMNH opened the Sant Ocean Hall,the museum's largest permanent exhibit and one that has been well received by the public. In September 2009 the museum expects to launch the companion Ocean Portal – an online destination to inspire ocean literacy. Targeting between 8-13 year olds middle-school teachers and young adults 18-34 year olds a high level of online participation is expected. In February 2009 the portal will just be starting to be built using Drupal,an open source content management system. The portal is expected to have extensive links to social media such as Facebook Twitter Digg etc. One hassle of using all of these online sites is managing the multiple registrations and keeping track of user IDs and password. There are several companies that are trying to solve this problem. This project would entail trying each of the options out and giving us feedback on the pros and cons (from the users' perspective) of each option. They include Facebook Connect and Open ID. If time permits the candidate would do research as the future of each possibility as well.

Qualification: This opportunity is best suited for candidates with experience using online interactions. This requires extensive familiarity with websites web 2.0 tools and social media and the ability to think through how various types of users (teachers students young adults etc) would use these new tools and whether they would be inclined to use any of the new registration systems and how information about the new systems should be incorporated into the Ocean Portal and presented to portal visitors.

Preparing a List of Endangered Plant Speciess

Code: NMNH-09

The Global Strategy for Plant Conservation (GSPC) calls for a preliminary assessment list of the conservation status of all known plant species. The intern will use specimen data from the U.S. National Herbarium to investigate and analyze preliminary conservation assessments on select plant families.

Qualification: Experience using Microsoft Excel. Must be able to work independently .

Bringing 21st century taxonomy to the Facebook universe

Code: NMNH-12

Facebook and other social networking sites have revolutionized the way students and the general public communicate with each other and share information. Drs. Terry Erwin and C.J. Geraci seek an intern who can develop an application that will share via Facebook images of beetles from the Ecuador Canopy Biodiversity Project. Our goal is to use our Ecuador canopy beetles as a tool to engage the public and demonstrate the science behind species descriptions and biodiversity conservation. We will provide raw images of our beetles and background text on the basics of taxonomy and methods of describing new species. The student will be charged with developing innovative ways to deliver those data to the Facebook universe in a legal ethical and educational manner. This project will enable the student to serve as a bridge between basic science and the developing field of online natural history education and outreach.

Qualification: The candidate must be familiar with computer programming and software involved with developing Facebook and other social networking applications. Experience in entomology and taxonomy not required but general biological science background is desirable. Must be creative and able to work in a team brainstorming environment.

Animalium Bibliography Reconciliation

Code: NMNH-13

This turn-of-the century important index to species names has been completely digitized and re-keyed. The multiple bibliographies need to be fully reviewed to point to the proper full titles of the books and periodicals listed. This entails reviewing Smithsonian's integrated library catalog system (SIRIS run on Sirsi/Dynix software) and the OCLC Worldcat database to find the bibliographic record that matches these publications. The titles that are the most relevant to taxonomic naming of species will be prioritized for scanning in the international project: Biodiversity Heritage Library (BHL).

Qualification: Comfortable in working with databases (MSAccess experience is a plus) attention to detail interest in bibliographic description foreign language reading skills desirable.

Water in volcanic glasses

Code: NMNH-14

Student will use Fourier Transform Infrared Spectrometry (FTIR) to measure water contents in volcanic glasses erupted on the sea-floor. The project is laboratory based requiring dexterity with small samples and attention to detail. Student will learn to use a petrographic microscope lapidary equipment and the FTIR instrument. The student will prepare samples if necessary identify mineral phases in volcanic glasses record FTIR spectra process the spectra and analyze and evaluate the results in the context of the global deep earth water cycle.

Qualification: Coursework in the physical and/or life sciences and prior laboratory work are pluses.

Fish Fintasies: Scanning Fish Illustrations and Images

Code: NMNH-15

The Division of Fishes seeks an intern to help scan selected illustrations from the Fish Illustration Collection. The Fish Illustration Collection is located at the Museum Support Center (MSC) in Suitland Maryland (a free shuttle service is provided from the Natural History Building) and contains original art photographs and other visual works depicting various fish species found throughout the world. The collection spans a time of more than 150 years and contains images that document live fish characteristics such as color and other external anatomical features that may not be distinguished in preserved specimens. Interns will reproduce original works in digital format for a myriad of imaging products including access to our images using our specimen database.

Qualification: Interns should have an attention to detail an interest in biological science and ability to handle fragile museum objects. Additionally interns should be able to scan images into digital format (tiff and jpg) using Adobe Photoshop and have a working knowledge of database software e.g. Microsoft Access.

Reformatting Fish Radiographs: Digitizing Radiographic Negatives

Code: NMNH-16

The Fish Division seeks interns to scan radiographs from the Fish Radiograph Collection. The collection is located at the Museum Support Center (MSC) in Suitland Maryland (free shuttle service is provided from the Natural History Building) and contains 25 000 radiograph plates imaged from our fluid-preserved specimen collection. The radiograph collection dates from 1950's and has images from thousands of fish species ranging from the primitive & slimy hagfish to complex but endearing puffers. Interns are needed to reproduce the plates in digital format create a spreadsheet to record metadata and if time allows insert the images into the multimedia module of KeEmu.

Qualification: Interns should have an attention to detail interest in biological science ability to scan images into digital format using Adobe Photoshop and working knowledge of Microsoft Excel.