Tuesday, January 26, 2016

The Return of Live Broadcast Experiments at UWYO

Join the fun and watch some live experiments being broadcast now from the University of Wyoming by Kim Miller and Brandon McElroy.

https://youtu.be/6biMhboBczA

Leave comments on the youtube site and provide your feedback to our science experiments!

Wednesday, January 20, 2016

January Newsletter

Dear Experimentalists,

We hope everyone is having a great start to the New Year.   We have exciting news to get 2016 started on the right foot!

This issue contains the following:

  1. 2015 Year in Review
  2. Events for 2016
  3. Three easy ways to get involved in EarthCube
  4. SEAD 2.0 Launch Webinar


2015 Year in Review
2015 has been a great year for SEN. In case you missed some of it, here are a few highlights.  We presented an invited talk at the 46th annual Binghamton Geomorphology Symposium with a corresponding paper in Geomorphology.   We also held our first graduate student and early career travel grant contest for funds to AGU.  This contest is the first of many that SEN will be funding.   We started broadcasting live experiments using YouTube so that scientists from around the globe could participate in data collection. At the AGU Fall Meeting this year, we spread the word about SEN and the Wiki by handing out buttons and stickers.  The Wiki (www.sedexp.net) saw many helpful updates as well as 81 entries to the Knowledge Base with 21 new accounts created on sedexp.net.  For more information on these events and others, please check out the archive on the SEN blog.

Events for 2016
SEN has many exciting events planned for 2016.  Here are a few that are currently in the works:
CSDMS/SEN Annual Meeting
SEN will be cohosting the Community Surface Dynamics Modeling System’s (CSDMS) annual meeting being held on May 17-19th, 2016 in Boulder, Colorado.  This year’s theme is Capturing Climate Change.  Keynote talks and hands-on clinics will focus on “advances in simulating the imprint of climate change on the land and seascapes, including the processes that influence them”. For more information or to register, please follow this link.

SEN Travel Grant Contest to CSDMS/SEN Annual Meeting
SEN is sponsoring a data-utilization contest for graduate-student and early-career geoscience modelers who feel passionate about advancing science through experimental data sharing and reuse. The top four winners of the data-utilization contest will have all travel and registration costs paid for. For more information or to register, please follow this link.

More Live Experiments
SEN will be broadcasting more live experiments this year.  Please stay tuned to the SEN twitter account (@sedimentexp) and the blog for updates and links to live feeds.  If you are interested in broadcasting your experiments, please email us (sedimentexp@gmail.com) and we can help you get set up.

Three easy ways to get involved in EarthCube  
Much of the funding from NSF's EarthCube program goes to projects developing technologies to aid in geoscience research.  Below are three ways you can learn more about, get involved with, and inform the future of these projects.

Not sure if EarthCube projects are useful for you?  
Check out the newly created "EarthCube Tools for Doing Geoscience" monthly webinar series (goo.gl/1E6gEJ).  An upcoming webinar on Friday, 1/22 at 2 PM EST (11 AM PST) will describe OntoSoft's efforts to train scientists in writing "Geoscience Papers of the Future" that document data and methods associated with published research.

Found a new technology of interest and want to learn more?  
If you are a graduate student or early career scientist, apply for an EarthCube "Visiting Scholar Travel Grant."  This will pay for you to visit the institution developing the technology to learn more about applying it to your research.  More information can be found here: goo.gl/UEydTb.

Feel like EarthCube isn't meeting your technical needs?  
Submit a Use Case.  This is basically a formal description of the technical needs for your research project.  Take two minutes to fill out a simple survey (goo.gl/As9NRh), then a member of EarthCube will follow up with you to conduct a phone interview.  The Use Cases will help to inform the funding and development of future EarthCube projects, so here's your chance to steer EarthCube toward building technologies that are useful for you.

SEAD 2.0 Launch webinar (1/21) 
SEN has been partnering with SEAD ("Sustainable Environment Actionable Data") to link our SEN Knowledge Base with their technical tools for storing data and making it discoverable.  SEAD is launching an upgraded version 2.0 and is hosting a webinar to describe their new release.  The webinar will be held on Thursday, 1/21, at 1:30 PM EST (10:30 AM PST).  More information is available here: http://sead-data.net/webinar-introduction-to-sead-2-0-the-next-generation-of-sead-data-services/

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

Happy experimenting,
The Sediment Experimentalist Network

Wednesday, January 13, 2016

SEN / CSDMS travel grant contest

The Sediment Experimentalist Network (SEN) is sponsoring a data-utilization contest for graduate-student and early-career geoscience modelers who feel passionate about advancing science through experimental data sharing and reuse. The top four winners of the data-utilization contest will have all travel and registration costs paid for their participation at the 2016 joint CSDMS (Community Surface Dynamics Modeling System) - SEN annual meeting in Boulder, CO, on May 17-19, 2016.


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: http://earthcube.org/group/sen


In contrast with past contests focused on submission of data entries to the SEN Knowledge Base (www.sedexp.net), the purpose of this contest is toward the utilization of Knowledge Base entries and the coordination of new collaborations between modelers and experimentalists through SEN toward achieving science goals.  In particular, how can sediment experimental data be utilized to inform, test, and refine models and predictions for earth surface processes?  This will be a major goal of this year’s joint CSDMS-SEN annual meeting on “Capturing Climate Change.”


Applicants will be judged primarily on the basis of a brief (2 page max) proposal describing how items in the SEN Knowledge Base can help to answer a science question of interest.  We particularly encourage contest entrants to try to track down data and existing experimental facilities and their capabilities listed on the SEN Knowledge Base.  If data can be found, we encourage descriptions of preliminary analyses in the proposal.  If data cannot be found or are difficult to use, please explain the problems you encountered and ways these problems might be addressed in future development of the SEN Knowledge Base.  If data do not exist but potential experimental collaborators can be found, please describe a collaborative project that can be coordinated through SEN. (Please note that we will be highlighting the proposals of successful applications during the CSDMS / SEN meeting.)


Eligibility
This contest is open to current graduate students and early career scientists (within 5 years of graduating) who are interested in advancing science through data sharing and reuse.


Requirements
  1. Sign up for the SEN Newsletter: http://goo.gl/s7dLjb
  2. Create a Knowledge Base account at www.sedexp.net
  3. Start browsing entries containing experimental data, set-ups, methods, and equipment relevant to your science question.
  4. Think of an earth-surface science question to be answered using experimental data and/or new collaborations with experimentalists and prepare your proposal as described above.
  5. Prepare an abstract for the SEN / CSDMS that mentions your proposed data utilization idea, and include this in your presentation at the meeting.  The data utilization idea does not need to be a central feature of your CSDMS presentation, but it should be included.
  6. Write a brief (one paragraph) professional biography.
  7. Deadline for submissions is April 1, 2016.  When registering for the CSDMS meeting, be sure to check the box to indicate that you are applying for the SEN / CSDMS travel grant.  Then, send your application materials (proposal, professional biography) to sedimentexp@gmail.com by April 1, 2016.


Selection of Winners
Winners will be selected on the following criteria:
  1. Originality of proposal.
  2. Depth of engagement with the SEN Knowledge Base.
  3. Applicability of proposal to planned presentation at CSDMS.
  4. Feasibility of proposal and qualifications of applicant toward proposed idea.
Winners will be notified via email and will be given instructions on the funding process. Names of winners will also be featured in the SEN Newsletter. Winners should acknowledge funding from NSF SEN when presenting their work at the CSDMS meeting.


Timeline
~January 15th: Contest opens
April 1st: Deadline for CSDMS abstract submission, registration, and SEN travel grant application
April 15th: Notification of winners
May 17-19th: CSDMS meeting (Boulder, Colorado)

Questions? Please contact SEN at sedimentexp@gmail.com.

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 onwww.sedexp.net.  The winners are:


Please be sure to check out all the great entries on the SEN wiki at http://www.sedexp.net.

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 sedimentexp@gmail.com.

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 athttp://sedimentexperiments.blogspot.com/ and follow us on Twitter (@sedimentexp).

Happy experimenting,
The Sediment Experimentalist Network
http://workspace.earthcube.org/sen

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

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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 sedexp.net
 
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 sedexp.net
The Knowledge Base/Wiki at www.sedexp.net 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 athttp://sedimentexperiments.blogspot.com/ and follow us on Twitter (@sedimentexp).
 
Happy experimenting,
The Sediment Experimentalist Network
http://workspace.earthcube.org/sen

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.