Archive by Author | Andrew Sallans

Profile of Notes from Nature Team Member: Mike Denslow

Name: Mike Denslow

Title: Assistant Director for Scientific Research Collections

Where do you work primarily? The National Ecological Observatory Network (NEON)

What you do in your day job? I am responsible for the archiving of biological samples collected as part of NEON’s field activities. Archiving is the act of safely saving and making available samples for use in research. NEON is an ecological observatory that will have 60 field sites across the Unites States (including Alaska, Hawaii and Puerto Rico) where ecological information will be collected for at least the next 30 years. These samples represent a range of organisms from mammals and plants to soils and zooplankton, just to name a few.   Now-a-days archiving not only deals with physical specimens and their safe keeping but also the digital information that goes along with them. For this reason, I am also concerned with capturing information about these sample in a digital format and making sure that it accessible on the internet for interested people to find and easily utilize.

What’s your role with NfN and what do you hope to gain from it?  If relevant, how will your research benefit?   My primary role at Notes From Nature is to bring in photographs of plant collections from various plant museums (called herbaria). I am also responsible for providing feedback on the design of the web interface for the project.   I am interested in developing new ways to make more information from museum specimens available for people to discover and use. My hope is that people will also appreciate the importance of museums in the process. There is a wealth of existing information about biodiversity that is not currently available in easily usable formats. It is critical that new ways of getting this information are developed and Notes From Nature is one exciting way that this is being done.

What’s the most exciting aspect of citizen science work from your point-of-view?  I really enjoy seeing the things that people notice about museum specimens and the questions that get generated from these observations. The contributors to Notes From Nature find all kinds of interesting things both on the labels and the specimens themselves. I am really enjoying interacting with people on the Talk page and it is helping me see museum specimens in a whole new way.

Video from CalBug

Like the CalBug portion of Notes from Nature?  Take a few minutes and view this video that they produced about the need for entomological museum collections and some of the challenges that they face.  It’s all part of the strategy for understanding global change.  See video here:  Global Change and CalBug

Shapely beetles on Notes from Nature

Are you curious about how Notes from Nature is actually making an impact on real scientific research?  One of our collaborators, Kip Will, a scientist with the CalBug team at the University of California – Berkeley’s Essig Museum of Entomology, offers some detail in a post on another blog.  Kip talks about how he uses the data afterwards, how one of his undergraduate assistants has been involved, and some of their preliminary results.  It’s great to know that all this citizen science work makes a difference!  – Andrew Sallans

See full post here:  Shapely beetles on Notes from Nature

Profile of Notes from Nature Team Member: Kip Will

Kip on expedition in Chile.

Kip on expedition in Chile.

Name:  Kip Will

Title:  Associate Director of the Essig Museum of Entomology and Associate Professor in the Dept. of Environmental Science, Policy, and Management.

 Where do you work primarily?  My research is on the systematics, taxonomy and evolution of a major, world-wide group of beetles (Carabidae). As a field biologist I travel to many parts of the world to sample them. Most of my time is split between the Southern Hemisphere (for example Australia or Chile) and the California region.

 What you do in your day job?  When classes are in session I teach the wonderful students of UC, Berkeley about insects, evolution, ecology, and behavior. I advise undergraduate and graduate students on projects that range from DNA sequencing to biological-illustration to observations of beetle behavior. I also take time to study the morphology and genetics of beetles in the laboratory and in the museum collection.

Photo of a Californian beetle, Pterostichus morionides.  By Kip Will.

Photo of a Californian beetle, Pterostichus morionides. By Kip Will.

 What’s your role with NfN and what do you hope to gain from it?  If relevant, how will your research benefit?  As one of the CalBug science team members, I will help to manage the specimen imaging and the flow of data back from the Citizen Science Volunteers. My research is entirely specimen-based and so having the valuable data from specimens in our collections digitally available for analysis will be a huge benefit to my research. One beetle group I am currently working on has about 125 species that are only found in western North America and most of these only in California. We have tens of thousands of specimens of these beetles to study. Once label data has been transcribed from these beetles I will be able to analyze the spatial relationships among these species at high resolution and look for trends in patterns over long (evolutionary) and short (ecological) timescales.

What’s the most exciting aspect of citizen science work from your point-of-view?    Being able to share the thrill of discovery and passion for science with such a broad audience is amazing for me. Also, with the help of volunteers, I now see a task I thought at best would take most of my lifetime could possibly be done in months. This is something of a dream come true.

Profile of Notes from Nature Citizen Scientist: “SandersClan”

Name:  Maggie (my userid is SandersClan).

Country of residence:  I live in the good ol’ U.S. of A.

What sort of science background or interest do you have?  I really don’t have a science background to speak of. I have always been fascinated by repeating patterns in nature, though. My family and I are fortunate to be surrounded by wonderful hiking areas, so we spend as much time outside as we can. We spend lots of time looking for and collecting fossils and interesting things.

What do you find most exciting about Notes from Nature?  I am so excited by Notes from Nature mainly because it’s not really repetitive. Each sample is unique, as is the description of where it was found and when. While I type, it’s easy to picture the area I’m transcribing, and it’s never the same as the one before.

What’s the most exciting aspect of citizen science work from your point-of-view?  I love citizen science because it’s an easy way to feel involved in something outside of my home and regular life, something ‘bigger’, if you will. I’m a homemaker, which means things feel the same from day to day. With citizen science I can participate in these projects at my leisure. I can invest as much time as I want, when I want, and my children can see that I have eclectic interests.

What other citizen science projects (including beyond Zooniverse) have you participated in?  I’ve participated mainly in Sea Floor Explorer, Ancient Lives, SETI Live and Cell Slider, but have dabbled in a few other projects as well. I have to say that I would love to see Zooniverse create kid-friendly projects, especially with summer coming!   Thanks for the opportunity to share!

 

 

 

 

 

 

 

What to do about insufficient information?

Today’s post is going to highlight a recent conversation amongst Notes from Nature citizen scientists regarding what to do when a specimen doesn’t seem to have most of the necessary information.  Is it best to just leave fields blank?  Is it better to just skip it?  Is it a “Top Secret” specimen?  These are great questions, and ones which will likely come up over and over again throughout the life of Notes from Nature.  Here’s the conversation.  How would you deal with this?

  • by carolely

    The label has only the scientific name and a question about that. Should I create a record and leave all the other fields blank?

    Posted 4 days ago
  • by SandersClan

    I vote yes.

    Posted 4 days ago
  • by ghewson

    Yes, then it’ll be flagged as needing more information.

    Posted 3 days ago
  • by carolely

    Thanks for the help. It seems I lost this page when I started this discussion so I never got to enter it. However, I’ll know what to do next time.

    Posted 2 days ago
  • by nosenabook

    I’m glad to know what to do as well, when I saw one like this, I passed on to the next specimen.

    Posted a day ago
  • by nosenabook in response to ghewson’s comment

    Responding to ghewson, it sounds like it is better to leave a field blank than enter “none given” say, for the reference. I started doing that because it was easier than arguing with the form – YES skip this field – and because R. K. Godfrey rarely gives a reference.

    I’ll leave that field blank from here on out, unless or until I hear different.

    Posted 21 hours ago
  • by xairbusdriver

    I seem to have found a “Top Secret” specimen, twice! 😉 If you come across Image ANN000039x, you’ll see what I mean. The ‘Location’ info seems to te a test site for White Out(r)! “…N side of _ Creek Road (S of Rte _), ca. air mi ESE of _. __________ of Sec ” I sure hope L. C. Anderson didn’t get into any trouble finding that specimen! 8) LOL!

    Posted 18 hours ago
  • by ghewson in response to xairbusdriver’s comment

    Ah yes, I had that, and tagged it #redaction. But if you search for that tag, there are 0 results! Spookyyyyyyyyyyyyyyy!

    Posted 17 hours ago
  • by SandersClan in response to xairbusdriver’s comment

    I can’t decide whether this is a Roswell, thing, the MIB, or what!

    Posted 16 hours ago

Imaging the University of Virginia’s Mountain Lake Biological Station Herbarium

Notes from Nature has been a significant undertaking with many people involved, but the transcription work being completed through the project is only a slice of the entire process of increasing access to and use of research collections.  This guest post comes from Christina Deane, Head of Digitization Services in the University of Virginia Library.  Christina was intricately involved with the imaging of the University of Virginia’s Mountain Lake Biological Station Herbarium, which is one of the current featured collections.  Through this post, we hope you’ll gain an understanding of how all of the images in this collection were produced.  If you are interested in seeing more about the University of Virginia Library’s Digitization Services, see this video:  http://www.youtube.com/watch?v=7CRHyj-6syM (look to 3:24 for a photo of a herbarium sheet!).  This story is one of many ways, and we will likely touch on other imaging processes in the future.  – Andrew Sallans


We began a discussion of how this project would be carried out in late summer of 2005.  The conversations included biologists, librarians, and technologists, to make sure that we were covering our bases on _MG_0323technique, metadata, and consistency so we would only have to do this once!  Once we had ironed out some of the metadata issues, we were able to modify our scanning workflow to accommodate the different requirements for the herbarium specimen.   We agreed that we would create archival tiffs and deliverable jpegs at 300 dpi following UVa’s digitization guidelines, and our digital library workflows were already in place to programmatically extract technical metadata from the images.

We hired a student in the spring of 2006 to begin scanning images using our overhead, Hasselblad cameras with PhaseOne P45 Plus digital scan back cameras (capturing at 39 megapixels!).  These cameras are typically used for our rare print materials, including all varieties of rare books, Jefferson letters, and even copies for the Declaration of Independence.  We established a set way to position the ruler and color bar so we could achieve a consistent look for the images, and this was likely influenced by other herbarium digitization projects going on at the time.  It was definitely a different way to work than what we were doing for books and manuscripts.  When we began this work, we didn’t really know how many specimen there were to scan, as the estimates we were provided with were in the thousands.

Our workflow was to barcode the images before scanning them, create a folder name based on the folder the items_MG_0314 were housed in, and name each image based on the barcode.  Our cameras and digital backs were very slow back in 2006, and imaging took a lot longer then than it does now.  Once through the basic quality assurance steps (QA) we were to send jpegs to the librarians in charge of the project so they could facilitate the metadata creation with the team they had assembled to work on this part of the project.  We utilized multiple rounds of QA so at least 3 or 4 people examined each image.

Scanning continued from the spring of 2006 through the spring of 2007, at which point the student working on the project graduated.  Scanning resumed in the spring of 2008.  Over the course of the next year, DS digitized thousands more images.  This _MG_0317process went faster because DS had acquired new camera systems with autofocus lenses and faster digital backs for almost instantaneous capture of the images.  During 2008 we continued scanning specimen as they were delivered to us.  We made a big push in January of 2009 to finish the rest of the collection (over 4000 pieces), and we completed the project that month. Full-time staff involved in the project included Andrew Curley, Kristy Haney, Jeanne Pardee, and Christina Deane.  John Ruscher was the primary student worker in the early part of the project, and many student employees were involved in the second phase of scanning from 2008 to early 2009.  Over the course of the project, we scanned 8,935 images in all.

-Christina Deane, Head of Digitization Services, University of Virginia Library

Featured Collection: University of Virginia’s Mountain Lake Biological Station Herbarium

Today, I’m pleased to offer another guest post from a colleague here at the University of Virginia, Michelle Prysby.  Michelle supports science education and outreach at UVA, but also has a special place in her heart for herbaria, master naturalist groups, and citizen science, having spent much of her academic career in those areas.  Upon my invitation, she eagerly jumped at the opportunity to help out with sharing the story of Mountain Lake Biological Station as part of UVA’s science education and outreach effort.  – Andrew Sallans


On a remote forested ridge, at 1,160 meters in elevation in the southern Appalachian mountains sits Mountain Lake Biological Station (MLBS), a busy hub for ecological and evolutionary biology research.  As part of the University of Virginia Department of Biology, MLBS serves as a facility for teaching field courses, a research site for scientists from around the country, and, for parts of the year, a home for students and faculty who come there to learn and to study.  Field courses include topics such as Wildlife Disease Ecology and Techniques in Conservation Biology, while research at the station has included studies of high-elevation forest ecology, genetics of various native and non-native plants, and salamander dispersal, to name just a few.

Courtesy of Special Collections, University of Virginia Library, Charlottesville, Va. Item RG-30/1/10.011

The station has some high tech research facilities, including a DNA extraction lab and chambers for growing organisms in controlled environments.  The first stop, however, for a scientist interested in studying plants in the area would likely be the much less high tech herbarium.  The MLBS herbarium houses more than 9000 plant specimen from the Mountain Lake area, the surrounding Giles County, and a smattering of other locations in Virginia and the Southeast.  It’s a great resource that gets used by many scientists studying plants at Mountain Lake.  Visiting scientists starting a new research study, for example, might comb through the herbarium to locate possible study populations of a particular plant.  A new graduate student might use the herbarium to help formulate research questions and choose a study system.  It’s also used for education, particularly during MLBS courses on plant conservation and diversity.

The herbarium has been assembled over time through collections by U.Va. scientists and through the acquisition of other scientists’ collections over time.   It has become a fairly extensive collection for the region, with significant contributions made by many different researchers.  It’s a region that is quite biologically diverse, too, with varying topography and microclimates.  Walking out from the station atop Salt Pond Mountain, one can find several forest types, rock outcrops, bogs, streams, meadows, and one of only two natural freshwater lakes in Virginia.

MLBSHerbarium

Photo of UVA Mountain Lake Biological Station Herbarium cabinet, taken by Andrew Sallans

The herbarium grows every year, particularly through the efforts of students taking the plant diversity course in the summers.  It contains some very old specimens—more than 100 years old.  Some of these species may no longer even exist in the locations where they were originally collected.  That’s one reason herbaria like the one at Mountain Lake are so important as both a reference collection and historical record.

The MLBS Herbarium is cared for by Eric Nagy, Associate Director of MLBS and Assistant Research Professor of Biology at U.Va., and by Zack Murrell, Associate Professor of Biology at Appalachian State University and instructor for the MLBS Plant Conservation and Diversity summer undergraduate field course.

“The herbarium is one of Mountain Lake Biological Station’s greatest assets,” says Nagy.  “Other field stations drool when they see what we have for our users.”  The digitization of the collections and the database of specimen information transcribed through Notes from Nature will make it even more valuable.

Mountain Lake Biological Station invites the public to its Open House event, July 13.  If you happen to be nearby, stop in to learn more about the research at the station and visit the herbarium in person.

-Michelle Prysby, Director of Science Education and Public Outreach, University of Virginia

Profile of Notes from Nature Team Member: Andrew Sallans

Name:  Andrew Sallans

Title:  Head of Strategic Data InitiativesAndrew

Where do you work primarily?  University of Virginia Library

What you do in your day job?  Unlike most of my Notes from Nature colleagues, I am not in a research or teaching position, and instead focus my energy on building services to support data-intensive research, working with researchers on data management problems, and facilitating the management, access, use, and preservation of research data with UVA researchers.  

What’s your role with NfN and what do you hope to gain from it?  If relevant, how will your research benefit?  I’ve been involved with Notes from Nature from its inception, having been the lead PI on a proposal to Zooniverse on behalf of SERNEC.  I’ve been working with SERNEC for around 6 years now, with an eye towards digitizing the local UVA biological collections and providing a proper, broader long-term home for the digital data output.  The opportunity to partner with the Essig Museum and Natural History Museum teams has been a real pleasure and opportunity to see other approaches for increasing access to biological collections, digitization methods, metadata standards, cataloging approaches, and general collection challenges.  I believe that these experiences will all be beneficial as we continue to develop and evolve research collection management strategies here at UVA.

What’s the most exciting aspect of citizen science work from your point-of-view?  This project has been exciting in many, many ways.  Although I’m not in the role of a scientist, I’ve had the privilege of interacting directly with many collections over the past decade in order to help manage and preserve those collections.  I’ve always loved being able to closely examine, understand, interpret, and contextualize items in collections, but this is something most people are never exposed to.  Even with many new programs to increase STEM research and education, it’s sometimes hard to develop enthusiasm when direct contact with science is sometimes too dangerous or costly for the student or scientific object; I’ve seen the same be true in libraries (ie. lack of interest in history because it’s all behind glass).  Zooniverse projects like Notes from Nature offer an excellent opportunity to make a meaningful contribution to scientific progress by completing critical tasks at a massive scale, while simultaneously having an opportunity to interact quite closely (ie. high-quality images are almost as good as the real thing!) with many specimen and the expert scientists and managers who work with them each day.  I’m hopeful that we’ll inspire new researchers and research projects and create some great conversations between those who are passionate about science.

Profile of Notes from Nature Team Member: Rosemary Gillespie

Name:  Rosemary Gillespie

Title:  Director of the Essig Museum of Entomology and Professor in the Dept. of Environmental Science, Policy, and Management.

Where do you work primarily?  My research looks at how species form and diversify, work that takes me to the isolated environments of remote islands of the Pacific, Indian, and Atlantic oceans. These islands serve as microcosms for the whole evolutionary process and also allow us to recognize the influence of humans and other vectors of change. I work mostly on spiders, in particular those that have radiated into myriad forms on the remote islands of the Pacific. To this end, I spend many days in the high elevation cloud forests of the islands, working mostly at night when the spiders are active.

What you do in your day job?  On a regular day, there are lots of things going on. I teach classes to some wonderfully enthusiastic groups of students and have meetings with diverse faculty to talk about directions of various initiatives, a particular current focus being on global change biology. With my students and postdocs, I discuss their projects, which range from the genomics of scorpion venoms to the diversity of sponges in marine lakes in Indonesia, and characterization of microbial communities to the description of new species of insects and spiders.

What’s your role with NfN and what do you hope to gain from it?  If relevant, how will your research benefit?  I became involved with NfN before I knew it existed! I was talking to a colleague, John Wieczorek, here at Berkeley’s Museum of Vertebrate Zoology, about the insurmountable problem of digitizing the massive numbers of insect specimen labels. John’s answer was to get them up on the web and ask for the help of citizen scientists. So we developed a protocol to get images of the labels up on the web – but how do we get them out to citizen scientists? This was when we discovered Zooniverse – over 2 years ago now. The first connections were made largely through the work of Joanie Ball, who is finishing her PhD here at Berkeley. And we’ve come a long way since then! Now that it’s up and running, what we can gain from it, first and foremost, is exposing the wealth of historical information to people who are ready to explore – and seeing how they engage with the material. The second is the use of the information provided – how it can be incorporated into the museum database to inform us about changes in biodiversity over the history of the collection.

What’s the most exciting aspect of citizen science work from your point-of-view?  The most thrilling aspect of this effort is connecting with people that are interested in exploring the opportunities and genuinely want to help the scientific enterprise. It’s so exciting to see the level of interest in making this very new and exciting endeavor actually become reality!

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