Thursday, November 19, 2015

November Newsletter

SEN November Newsletter

Dear Experimentalists,

We hope everyone is having an excellent fall.  We have a lot of exciting news and upcoming events to share with you in this newsletter.

This issue contains the following:
  1. New NSF Data Policy
  2. Open Science Framework
  3. Travel Grant Winners Announced
  4. SEN at AGU Fall Meeting
  5. EarthCube Science Committee Webinar Series
  6. EarthCube Early Career Travel Grants
  7. Gilbert Club 2015
  8. EarthCube needs your help to gather examples of technical obstacles in geoscience research

New NSF Data Policy 
NSF is putting into effect a new policy on public access on January 25, 2016.  This policy will be required for all research funded by NSF and should help make it easier for the public to discover data and results from funded projects.  An FAQ on the new policy can be found here.

Open Science Framework
Raleigh Martin recently added a blog entry describing the Open Science Framework (OSF), a useful tool for data and workflow documentation through the research lifecycle.  This blog entry is based on a recent webinar on the OSF hosted by DataOne.

Travel Grant Winners Announced
Thank you to all the participants of the SEN Graduate Student and Early Career Travel Grant Contest.  We received many great applicants with excellent entries  The winners are:

Please be sure to check out all the great entries on the SEN wiki at

SEN at AGU Fall Meeting
For all those that will be attending the AGU Fall Meeting this December in San Francisco please be sure to check out the following SEN-related events.  During these events, SEN will be handing out buttons and stickers so you can show your support!

  • SEN team members will be available to the EarthCube booth (#116) in the exhibit hall.  The booth will be open from 10 AM – 5 PM on Tuesday, Wednesday, and Thursday.  Raleigh Martin will be there from 10-11 on Tuesday, and Kim Miller will be there from 10-11 on Thursday. 
  • Check out the oral and poster sessions entitled “Experimental Studies in Surface Processes”.  Oral sessions are being held Monday, December 14thfrom 1:40pm to 3:40pm and 4:00pm to 6:00pm in Moscone West 2005. The poster session is Tuesday, December 15th from 8:00am to 12:20pm.
  • We would also like to point out several other AGU events of potential interest to the SEN community:
    • AGU will be hosting a “Data Fair” at the Fall Meeting, which will include daily panel discussions on Geoscience Data Publishing and Repositories.  More information is available here.
    • EarthCube will be hosting a Town Hall (TH15D) on Monday (12/14) from 6:15-7:15 PM in Moscone West 2008 on “EarthCube Science Drivers and Implementation Roadmap”.
    • A technical session entitled “Data Ought Not Be in the Darkness: They Should Be Open, Accessible, Transparent, and Reproducible” will be held on Monday and Tuesday afternoons.  Search for session numbers IN23E and IN33A for more information.

EarthCube Science Committee Webinar Series
The EarthCube Science Committee will host the first in a series of webinars on "Doing Geoscience with EarthCube Tools" aimed at connecting geoscientists with products generated by EarthCube funded projects.  The first webinar will be held Friday, November 20, at 2 PM EST, with Kerstin Lehnert / Megan Carter (Lamont-Doherty Earth Observatory) presenting together on the iSamples Research Coordination Network, which seeks to improve discovery, access, sharing, analysis, and curation of physical samples and their associated data in the geosciences. Call-in and event details are available here.  More information on the webinar series is available here.

EarthCube Early Career Travel Grants
Two types of travel grants are now available to support early career scientists in travel to AGU and other conferences.
  1. The EarthCube Science Committee is offering six (6) travel grants of $500 each specifically for the upcoming AGU Fall Meeting.  Application deadline is November 30, 2015.  More information is available here.
  2. The EarthCube Engagement Team offers travel grants on a rolling basis. More information is available here.
If you are an early career researcher who has participated in SEN activities, or are planning to participate in more SEN activities, let us know if you have any questions about this travel grant at

Gilbert Club 2015
The annual Gilbert Club meeting takes place at the Berkeley Hall of Science the Saturday following AGU and features talks and discussions from prominent scientists in the field of geomorphology.  This year’s meeting features presentations from Sue Brantley, Eric Lajeunesse, and Sean Willet.  For more information, including schedule, registration, and transportation, please check out there website.

EarthCube needs your help to gather examples of technical obstacles in geoscience research
Is your geoscience research limited by computing or data management issues?  The goal of EarthCube is to break up these logjams that limit scientific productivity.  To address technical limitations in the geosciences, EarthCube is compiling a list of "Use Cases" (real-world examples of computing challenges) that will inform creation of cyberinfrastructure for the geosciences. Please fill out this form to describe your Use Case, then a member of EarthCube will follow up with you to conduct a one hour interview to gather more details about your Use Case.

For up to date information about SEN, please check out our blog at and follow us on Twitter (@sedimentexp).

Happy experimenting,
The Sediment Experimentalist Network

Thursday, November 12, 2015

Open Science Framework (OSF): A useful free tool for data and workflow management for scientific reproducibility

On October 13, 2015, DataOne hosted a webinar led by Courtney Soderberg from the Center for Open Science.

The webinar had two goals: (1) To outline the issues with existing scientific workflows that can lead to bias and results that are not reproducible, and (2) To introduce the Open Science Framework (OSF) as a tool to overcome these biases and increase the reproducibility of science.

Regarding issues of reproducibility, most scientists are probably aware of the narrow issue of computational reproducibility, i.e., the ability to take the data collected by a team of researchers, perform the same analyses, and reach the same conclusions.  Ms. Soderberg described this issue in her talk, but she also described more subtle biases and issues with reproducibility.  One issue is publication bias: analyses often change through the course of a project, and only the final (successful) analyses and results are documented, while negative results or dead-end analyses are never captured.  Related to publication bias is Hypothesizing After Results are Known, or HARKing.  To present a succinct story, publications often present hypotheses as a priori, whereas hypotheses may in fact have been generated after researchers spent significant time poring over the data.  In what is known as researcher degrees of freedom, data processing and analytical decisions are often made after seeing and interacting with data, severely increasing the potential for false positive outcomes, often outside of the awareness of a researcher.  (For further discussion of reproducibility problems, I suggest the enlightening recent special issue of Nature on this topic.)

In response to these various potential sources of bias, the OSF, a free web-based resource for data and workflow management, builds in mechanisms to reduce (or at least document) potential sources of research bias.  The OSF is meant to be used through the whole research life cycle, from project conception to final paper and data publication, and all actions taken, wiki entries written, and files uploaded on the OSF are timestamped and version controlled.  For example, it is possible to document a timestamped hypothesis prior to data collection and analysis to avoid HARKing.  More details on the OSF can be learned by viewing Ms. Soderberg's excellent presentation in full; below, I provide a few highlights:

  • OSF pages can be public or private, and there is granular control over access to individual pages and sections for collaborators or the general public.  Public projects are fully searchable.
  • Built-in tools smooth the collaboration process.  One can create templates for common file types, and projects can be "forked" to create copies of files/folders with original content intact.
  • Third-party software such as GitHub, Google Drive, and FigShare can be seamlessly integrated through add-ons.  This is especially useful for large files that exceed the current 128 MB limit for individual files stored with OSF (no total storage limit across all files).  The one catch is that, while all file versions uploaded directly to OSF are stored permanently, linked third-party content remains stored with third parties subject to their version control/storage policies.  Nonetheless, OSF does keep track of all version changes (even if it does not keep the original files).
  • Permanent identifiers (GUIDs) are assigned to projects created on OSF.  Other unique identifiers (e.g., DOIs, ORCID, LinkedIn) can be assigned to projects and/or researchers.
  • Versions of a project can be "registered" at a fixed point in time, such as when submitting an article for publication.  Registered versions become read-only and fully include all linked (third-party) content, so a registered project can provide a stable data/workflow accompaniment to a published journal article.  Registered versions can remain private for an embargo period of up to four years.  Once public, registered projects can be assigned a DOI.
  • Data sustainability is extremely important to OSF.  In case the Center for Open Science disappears, a "sustainability fund" has been established to maintain existing data in a read-only format indefinitely.
  • Public projects are fully searchable.

I strongly encourage all scientists to investigate OSF as an option for workflow and data management.  The advantage of OSF is that it provides a flexible, robust architecture for many data management challenges.  The disadvantage is that it may not fulfill discipline-specific needs of sediment experimentalists.  As we continue to develop the SEN Knowledge Base, we will closely follow developments of OSF and other data management platforms.

Raleigh L. Martin
UCLA Dept. of Atmospheric and Oceanic Sciences


Click here to view the webinar on the DataOne website.

Wednesday, September 30, 2015

SEN Fall Newsletter

Dear Experimentalists,
We hope everyone had a productive summer and are getting geared up for an exciting fall with the Sediment Experimentalist Network.
This issue contains the following:

  1. Graduate Student/Early Career AGU Travel Grant Contest
  2. Binghamton Geomorphology Symposium Update
  3. EC3 Field Trip Report
  4. New Features and Updates on
Graduate Student/Early Career AGU Travel Grant Contest
The Sediment Experimentalist Network (SEN) is sponsoring a data-sharing contest for graduate students and early career scientists who feel passionate about making their data public. The top three winners will be awarded travel grants in the amount of $1000 for use towards the 2015 American Geophysical Union (AGU) Fall Meeting.  The deadline for entries has been extended to October 15, 2015.
Binghamton Geomorphology Symposium Update
This September, SEN attended the 46th annual Binghamton Geomorphology Symposium hosted by the University of Buffalo.  This year’s theme was Experiments in Geomorphology and featured tours of various lab facilities and talks covering a wide range of experiments (photos).  SEN’s own Brandon McElroy presented a talk on our recent Geomorphology paper.  Wonsuck Kim, Raleigh Martin, and Kim Miller presented posters, which can be viewed here.
EC3 Field Trip Report
SEN team member, Raleigh Martin, recently attended a field trip hosted by EarthCube Building Block EC3, Earth-Centered Communication for Cyber-infrastructure, which focuses on the challenges of field data collection, management, and integration.  Check out the blog post to read about what we as experimentalist can learn from the field about data sharing.

New Features and Updates on
The Knowledge Base/Wiki at now has an entry category for “Lab Facility”, which can be linked to equipment entries.  Use these entries to promote your lab or find other lab facilities for collaborations. 
Also, there have been several new entries over the last month including: Erosional landscape topography by Kristin Sweeney, Field saltation observations by Raleigh Martin, and Data for experiments in high-intensity bedload transport by Ricardo Hernandez.
For up to date information about SEN, please check out our blog at and follow us on Twitter (@sedimentexp).
Happy experimenting,
The Sediment Experimentalist Network

Tuesday, September 29, 2015

Raleigh Martin at EC3 Workshop 2015

Recently I participated in the EarthCube funded EC3 (Earth-Center Communication for Cyberinfrastructure) workshop at Yosemite National Park and Owens Valley, California.  The workshop brought together a mix of geoscientists and computer scientists to address challenges in field data collection and to brainstorm cyberinfrastructure solutions to make field data collection easier, more efficient, and more likely to result in useful long-term data preservation.

My own work encompasses both laboratory experiments and fieldwork on active sediment transport processes.  Through my engagement with SEN (Sediment Experimentalists Network), I have already thought substantially about laboratory issues, so participation in the EC3 trip gave me a chance to think more about field data.  To my somewhat surprise, the idea of “fieldwork” varies vastly among domains.  Whereas fieldwork for me primarily encompasses collection of instrumental time series records, during the EC3 trip the focus was on mapping of geological structures and stratigraphy.

Despite my somewhat outsider status, I learned several lessons from the EC3 field trip, which I hope to share with the SEN community:

1)   The most effective development of geoscience cyberinfrastructure occurs when software developers and geoscientists are tied together at every step of the development process.  Otherwise, there is a danger that computer tools will not be compatible with the way that scientists actually do their work.  For example, tablet-based apps might one day replace the field notebook, but only if they accommodate the free-form sketches that don’t fit neatly into metadata categories.
2)   Research progresses in an unpredictable, heterogeneous, iterative, and “messy” way that makes the adoption of uniform, comprehensive cyberinfrastructure and database tools impossible.  I could see this in how much my concept of “fieldwork” differed from other workshop participants.  Rather than seeking a grand solution to all of our data problems, we’re better off building smaller-scale solutions for specific applications, then linking these applications through semantics, i.e., clear, machine-readable assignments of meaning that allow computers to link together heterogeneous databases into shared resources.
3)   Computer scientists actually enjoy our data problems and view them as research challenges!  They are not simply contractors for hire to build specific pieces of software.  As geoscientists, we can view work with computer scientists as research collaboration, which includes applying for grants together and writing papers together.  This will also make the development of cyberinfrastructure feel more like fun and less like a chore.  The EARTHTIME project is one great example of the synergies to be found between geoscientists and computer scientists.

These lessons are my own personal opinions, and I’m open to debate with those who might disagree!  I encourage comments on these ideas and perhaps even further blog posts by members of the Sediment Experimentalist Network on this topic of development of cyberinfrastructure for the geosciences.

Wednesday, September 2, 2015

DEADLINE EXTENDED: SEN AGU Graduate Student/Early Career Travel Grants

The graduate student and early career travel grant contest deadline has been extended to October 15th!  We are sponsoring a data-sharing contest for those who feel passionate about making their data public (more details below). The top three winners will be awarded travel grants in the amount of $1000 for use towards the 2015 AGU Fall Meeting.  Post your entries to and submit your application!


The Sediment Experimentalist Network (SEN) is sponsoring a data-sharing contest for graduate students and early career scientists who feel passionate about making their data public. The top three winners will be awarded travel grants in the amount of $1000 for use towards the 2015 American Geophysical Union (AGU) Fall Meeting.

The Sediment Experimentalist Network (SEN) is funded by the U.S. National Science Foundation (NSF) EarthCube program as a Research Coordination Network (RCN). SEN integrates the efforts of sediment experimentalists to build a knowledge base for data collection and management. The network facilitates cross-institutional collaborative experiments and communicates with the research community about data and metadata guidelines for sediment-based experiments. This effort aims to improve the efficiency and transparency of sedimentary research for field geologists and modelers as well as experimentalists. More information is available here:

The contest will be judged on the quantity and quality of participation in the SEN Knowledge Base (, which contains data catalog entries and descriptions of experimental setups, methods, equipment. To begin, create an account on the website and then start creating entries for your experiments. The more entries, the more likely you are to win!


This contest is open to current graduate students and early career scientists (within 5 years of graduating) who are interested in helping make data more accessible.


1.    Sign up for the SEN Newsletter:
2.    Create a Knowledge Base account at
3.    Start posting entries of your experimental data, set-ups, methods, and equipment.
4.    Send a one-page document to as described below 

Contest Entry

To enter the contest, please send a one-page document containing contact information, short professional biography, and a list of your SEN Knowledge Base entries to 

Selection of Winners

Winners will be selected on the quality (completeness of entry) and quantity (total number of entries) of entries to the SEN Knowledge Base. Winners will be notified via email and will be given instructions on the funding process. Names of winners will also be featured in the upcoming SEN Newsletter. Winners should acknowledge funding from NSF SEN when presenting their work at AGU.

REVISED Timeline

June 15th: Contest opens
October 15th: All entries must be received
November 1st: Notification of winners

Questions? Please contact SEN at

Thursday, August 20, 2015

SEN Travel Grant and Upcoming Events

Dear Experimentalists,

Hope you all have had a productive summer.  We just want to send a quick reminder about two upcoming SEN activities.  A full newsletter will be sent out at the end of September.

SEN AGU Travel Grants

The graduate student and early career travel grant contest deadline is soon approaching on August 31st.  We are sponsoring a data-sharing contest for those who feel passionate about making their data public. The top three winners will be awarded travel grants in the amount of $1000 for use towards the 2015 AGU Fall Meeting.  Post your entries to and submit your application!

Binghamton Geomorphology Symposium

Members of the SEN leadership team will be presenting a talk and posters at this year’s upcoming Binghamton Geomorphology Symposium, taking place on Friday, September 18 to Sunday, September 20, 2015 in Buffalo, NY, with the theme of Laboratory Experiments in Geomorphology.

See the second circular and more information at

Can’t make the symposium?  Not to worry; SEN presentation slides and posters will be made available in the next newsletter. 

For up to date information about SEN, please check out our blog at and follow us on Twitter (@sedimentexp).

Happy experimenting,
The Sediment Experimentalist Network