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National Moth Week

Did you know that July 20-28, 2013 is National Moth Week?  You can take your love of the Notes from Nature CalBug moths beyond transcriptions by participating in moth observations in the natural world.  Check out details for participation here:  http://nationalmothweek.org/

A look at some Notes from Nature stats

The Notes from Nature project has been running for almost two months already and we are still just excited as the day we launched. The community has been great and we have received some amazing support and feedback from many of you. We are actively working to expand our collection coverage and hope to keep you all entertained through all the beautiful summer evenings ahead of us. With that said, we thought it would be a nice moment to take a look at some of the trends of our community. This serves a both a peek behind the curtains as well as a sort of snapshot that we can return to in the future to see what has changed and how we improve over time.

We had the idea for this post since the day we flipped the switch and made the site live. We all knew that the first hours of the project being live were going to get some of the heaviest traffic we would experience. We wanted to do a little analysis of how that traffic came and left the site, we collected a small set of data over the first five days of the project in order to look at this. First things first, take a look at global the Notes from Nature contributors were over just the first five days (click to see in interactive map)!

Next, we thought it would be fun to take a look at how the site accumulated new users over the time after launch,

We see the expected, early gains in user numbers followed by a slower accumulation later in the week. After the really early spike in transcriptions that came with all the users, we saw a nice continuous growth of total transcription activity through the week.

We thought it would be pretty neat to look at the transcriptions coming in at different times of day from our two primary regions, North America and Europe.

The above graph’s X axes is in EST, so you can see a nice rhythm to the Notes from Nature transcription. We really like this graph and will love to see it play out over the course of a year or more! We built the above graphs with D3 and CartoDB, if you click on them you can see each one and take a look at the code used to create them.

So how is Notes from Nature doing more recently? Well, in the first five days we had around 5000 unique participants. In the past two weeks we have had just over 3200. Not bad! Projects like Notes from Nature usually get a lot of members early that don’t end up sticking around, but we have done well to keep them or create new ones over the small time period. Our biggest audiences are still overwhelmingly in the USA and UK.

Right now, we are averaging 1400 classifications per day! As we improve the interface and add new and interesting components to the mission, we think we can see a growth in this number, but we are really happy with it so far. We have completely finished, including replicate transcriptions, 12% of our records in only two months! We will have more records in the future, but hopefully we will have a bigger community working with us too. We are closing in on 200,000 transcription, which is going to be an amazing achievement. Thanks to all of you who are helping us do something amazing for biodiversity research, museum informatics, and science!

Calbug’s Dragonfly Research

If you are working on Calbug transcriptions, you’ve probably seen some dragonflies and damselflies pop up.  So, I wanted to take the opportunity to let you know how I’m using data from these specimens in my Ph.D. research.

But first, why study dragonflies?  First of all, these charismatic aquatic insects have been well-collected over time, making them good subjects for studies of change in community composition and distribution. Dragonflies also have a range of known pollution tolerance-levels and are useful indicators of general habitat degradation for freshwater habitats. They may be particularly good indicators of biological effects of climate warming. Studies in Great Britain have shown that the ranges of many species have expanded, range boundaries have shifted northward, and first-flight days are occurring earlier as a result of climate warming since 1960. Many of these changes are occurring faster or are more pronounced than in other groups. For example, one study found that dragonflies in Britain have experienced range shifts averaging 88 kilometers (km) northward, compared to 53 km for butterflies. Overall, dragonflies tend to like warmer habitats, and their high dispersal ability may allow them to respond more quickly to climate warming. At the same time, some species, usually those specialized for stream habitat or certain types of wetlands, are experiencing significant range reductions.

Eight-spotted Skimmer, perching. Photo © Ray Bruun

Eight-spotted Skimmer, perching. Photo © Ray Bruun

California is an interesting place to study changes in aquatic insect communities, because this relatively dry region has experienced drastic changes in aquatic habitat over the past 100 years. For example, irrigation for agriculture across the previously dry Central Valley has created more permanent freshwater habitats throughout the summer. The state has also experienced a dam-building frenzy over the past 100 years… 1400 dams now block the flow of every major river and most minor ones across the state. This eliminates significant portions of flowing water habitats and increases the amount of lake-type habitat. The human population of California has also dramatically increased from around 2.7 million to 37 million people over the past century. So, water demand is high and landscapes are becoming more and more dominated by urban areas and agriculture. So, how are these changes influencing plants and animals?

My research addresses this question by focusing on dragonflies and damselflies, collectively known as Odonata or “odonates.”  In one study, I’m using the locality and date information for each specimen in our collections to compile species lists for different California counties and time periods. The goal is to identify changes in odonate communities—such as species richness and the percentage of habitat specialists versus generalists—from the species lists, and identify species that are expanding or contracting in distribution. Museum collections, however, have some problems with their data, as you probably are beginning to realize after participating in the data entry! One is that collecting effort varies for different regions and time periods based on the interest of collectors. We can try to correct for this using a combination of statistics and smart data selection. For example, some researchers have used a relatively new statistical method that incorporates the length of species lists for sites or regions as a measure of effort for that area. This assumes that regions with longer lists had higher effort (an assumption that often, but not always, holds true). In regions with short lists, you would expect to find more species than were actually present in the records. In particular, some species that are harder to find or are less common may occur in more regions than what is represented in the collection. After accounting for effort, the ultimate goal is to determine whether changes in landscape variables, such as temperature, precipitation and human population influence communities across regions.

I have also resurveyed sites originally sampled by C.H. Kennedy (a collector you may come across!) in 1914. While he left comprehensive lists of species collected at specific sites throughout California and Nevada, he did not indicate the dates that he visited each site in his notes!  So, I used information from the specimens to reconstruct specific dates that Kennedy sampled each site, and then visited the sites within a week or so of the original sample date. In preliminary work comparing his surveys to my own, I have found that communities are becoming more similar across sites—we are seeing a homogenization of dragonfly communities, which may reflect the spread of urban and agricultural landscapes.

Hopefully, this gives you a taste for how we might use some of this data. We will keep you posted on the results!  And, feel free to email me, at jball@berkeley.edu , for more information on this research.

– Joan Ball

Calbug fields and photos

Recent comments and questions in the discussion boards have drawn our attention to aspects of transcribing that were not clear. So, we changed a couple of things.

First, we removed the Host, Latitude and Longitude fields, because many of our labels do not contain this information.  Instead, we added an “Other Information” field where you can enter any information that is not included in the other fields. As explained in the help text, this includes things like the collecting method (e.g. malaise trap), collecting times, name of host plant, etc.  Previously, it was unclear whether you should enter locality information exactly as on the label or if you should interpret information, like abbreviations. Because many people are transcribing this highly-variable information, we would like you to enter the locality exactly as it says on the label. Otherwise, we will end up with multiple interpretations of the same locality. One exception is if there is an obvious misspelling that is not an abbreviation—it would be helpful if you use the correct spelling. Please keep looking up the country, state and county information if they are missing from the label. But, keep a lookout for locations with multiple potential counties, and do not enter a county if this is the case.

In the future we may call on you again to help us geographically reference (“georeference”) these localities. That is, determine the latitude and longitude of the localities and estimate the uncertainty around those points. It makes more sense to us to wait until we have completed the data entry so that we can group the records by locality and georeference each locality just once.

You may also have noticed that the photo quality for some of Calbug’s recent photographs is not very good. That’s because when Calbug started, we used different methods for photographing and a different type of camera. Don’t worry, the bad photos will be increasingly rare in the future.  To get an inside look at how we are taking photos now, check out this instructional video that we made last year for students and staff imaging our insect specimens.

-Joan Ball

What happened to the transcription progress?

One of the questions we have been grappling with at Notes from Nature is how to add more specimen images to the application while still showing a clear path of overall transcription progress.  On the one hand, we have many more specimen images lined up from both CalBug and SERNEC, and need to keep expanding the pool of interesting and scientifically important collections being transcribed.  On the other hand, we don’t want Notes from Nature citizen science transcribers to become frustrated by a seemingly bottomless pool and confused by constantly increasing and decreasing progress bars.  In attempting to address this challenge, we’re going to do some small tests.  We’ve added some new specimen in recent days, and would like to hear what you think about these additions.  Among the new additions, we have about 74,000 new bugs, including many bombardier beetles, dragonflies, and damselflies, as well as about 13,500 new plant specimen.  Do you like that we’ve added these new specimen images?  Were you worried by the drop in transcription percentages?  Should we work to complete “missions” with smaller subsets before adding more content?  Whatever the case, check out the new specimen on Notes from Nature!”

Tending Our Notes from Nature Garden

Sometimes in the shuffle of getting things done, we forget to explain the simplest things.   For example, where do all these images come from?  Are there more to do when these are done?   What the heck is a CalBug or a SERNEC?

So lets answer some of these questions as best we can.  As we mentioned in the “About” section of Notes from Nature, CalBug and SERNEC are both regional consortia of natural history collections — CalBug focused on western North American (predominately) insects and SERNEC on southeastern United States plant specimens.

Lets turn to the SERNEC records first.  Right now the following herbaria  (or single plant collection) are featured on the site:  The R. K. Godfrey Herbarium at Florida State University, with 8,368 specimen images available and the Mountain Lake Biological Station Herbarium at the University of Virginia with 6,990 specimen images.  Soon we plan to load a third collection of 13,511 images from the herbarium at the University of South Alabama.   This represents a small proportion of the millions of specimens found in southeastern United States herbaria, so there is still a LOT of work to do here.

CalBug has about 230,000 images already taken,of which ~33,000 have been already made available via Notes from Nature, with another 28,000 to be added shortly.  These mostly come from the Essig Entomology Museum at U.C. Berkeley but also from U.C. Riverside and the California Academy of Sciences.  CalBug will also be adding more images in the future.   The ones there now represent a select group of insect taxa including: bombardier beetles  (genus = ‘Brachinus’ or genus = ‘Metrius’), cuckoo wasps (family = ‘Chrysididae’), odonates or dragon flies,  (order = ‘Odonata’), skippers (family = ‘Hesperiidae’), and tiger beetles (genus = ‘Cicindela’ or genus = ‘Omus’ or genus =’Amblycheila’).

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

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

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