What questions can we answer with SEN?

Thanks goes to Kim Litwin-Miller, who recently joined SEN as a postdoc, for this new image of SEN. The dark days in the lab are fading.

Here are some questions that SEN has been addressing and sharing with our network:

Q: Where can I buy the sediment I need for my experiments?
A: Check out our Sediment Resource list, compiled from SEN members.

Q: How can I set up an IP camera to stream my experiments?
A: Charles Nguyen's team at St. Anthony Falls Laboratory has shared their method for live streaming experiments on the SEN wiki.

Q: What's the best way to share my experimental videos?
A: This old blog post reviews different options for sharing experimental videos.

Q: How can I get a citable DOI for my dataset, and show the citation statistics on my CV?
A: Old blog posts and tweets have mentioned SEAD, figshare, and impactstory, sites that help you manage, publish, and track citation of datasets.

Q: How can I version and document my code so that I'll understand what I did 6 months from now?
A: We are embarking on the journey of learning GitHub and having our own code repository, to help with versioning, documenting, and sharing of code. The GeoSoft project is helping us out. Stay tuned for more info!

Sign up for our ~monthly newsletter or follow us on twitter (@sedimentexp) to get more information like this delivered to you.

Ask us a question (sedimentexp@gmail.com) that you want answered by the network!

SEN December News: Data publishing and sharing, workshops, and SEN on GitHub

Dear SEN,

We've made it to December. Hope the SEN Newsletter has brought you some useful information in 2014 (see the archive here), and we look forward to more experiments in 2015.

Some events and activities to consider:

• Town Hall on Publishing and Sharing Earth Surface Process Data @AGU
• Workshop on Modelling mixed-sediment river morphodynamics
• Sharing SEN research codes on GitHub
• What does SEN going Dutch look like? Utrecht Workshop

Town Hall

TH13D: Publishing and Sharing Earth Surface Process Data
Monday, December 15, 2014,12:30 PM - 01:30 PM
Moscone West 2008

We invite both data sharing rookies and professionals to come and discuss needs, obstacles, and existing resources.

Join us for a discussion on publishing and sharing Earth Surface process data. The session goal is to agree upon a set of descriptive fields for proper curation and efficient reuse of Earth-surface related data for experimentalists, modelers, and field investigators. Guidelines will be developed to support our community in preserving, sharing, and publishing data more consistently despite disparate research methods. We will use Sediment Experimentalist Network (SEN) laboratory experiments as an initial example but seek commentary from the broader EPSP community. Students and early career investigators are especially encouraged to attend.

If you have any concerns or questions about this topic in advance of the town hall, we'd be happy to hear about them: sedimentexp@gmail.com.

Workshop on Modelling mixed-sediment river morphodynamics

From abrading particles to river profile concavity...
27-28-29 May 2015
Water Lab, Faculty of Civil Engineering & Geosciences
Delft University of Technology, Delft, Netherlands

In the workshop we will discuss topics that deal with modelling mixed-sediment fluvial processes, covering a wide range of scales.

For more information visit the workshop event page.
To receive future circulars, contact the organizers, Astrid Blom (astrid.blom@tudelft.nl) and Enrica Viparelli (viparell@cec.sc.edu).

Sharing SEN research codes on GitHub

"If you write code for research, you’re missing out if you’re not on GitHub."
Read more about GitHub for sharing research code: http://blog.impactstory.org/impact-challenge-research-software-github/

In collaboration with the GeoSoft project, SEN has launched a GitHub repository and is looking for members! Let us know if you have a GitHub account, and we'll send an invite to join the repository (notify sedimentexp@gmail.com with your username). In the coming months, we'll be sharing scripts from our Community Experiments. SEN members may also post any code they'd like to share.

What does SEN going Dutch look like? Utrecht Workshop

While we work on finalizing the workshop report for sharing with you all, take a look at some Photos and Tweets from November's SEN Utrecht Workshop. Many thanks to Joris Eggenhuisen and the team at Utrecht for their critical support of this workshop!

Data are messy

"Science rarely proceeds as expected or hoped" begins Raleigh Martin's poster, titled "Data are Messy: thoughts from sediment experiments in the lab and field" and presented at the SEN Utrecht workshop in November 2014. 

Raleigh offers thoughts and recommendations on the "messy side of research", including "There's a lot of voodoo in methods" and "Many experiments are failures," and concludes: "There will be no "one-size-fits-all" solution for documenting experimental data and methods. This requires ongoing discussion that directly considers broader scientific objectives!"

The poster does a great job illustrating some of the challenges involved in properly managing and documenting data and methods in experimental geomorphology.

See the full poster here:

Data are messy: thoughts from sediment experiments in the lab and field, Raleigh Martin, 2014

SEN Workshop 2 at Utrecht University

Dear SEN community,

We are excited about our upcoming Sediment Experimentalists Network (SEN) workshop at Utrecht University: “Experimentalists going Dutch: Exploring the life-cycle of sedimentary experiments,” on November 4-7, 2014. We are particularly grateful to Joris Eggenhuisen and his staff for hosting this event and putting together an interesting program of discussions, talks, and community experiments.

If you will not be participating on-site in the workshop, that’s OK! We will be performing community experiments on delta formation and encourage off-site participants to provide input on how we will run these experiments, to view the experiments as they are running, and then to participate in community data analysis following the workshop. Furthermore, we invite off-site participants to join workshop discussions on data management, laboratory methods, and the experimental life-cycle. Please check our website on the EarthCube workspace for up-to-date information on these activities.

To ensure that off-site participants are not left out of any of the fun, please complete this brief Google Docs form to be added to our participant list for the event. Please note time differences! (UK: -1 hour, US East: -6 hours, US Central: -7 hours, US Mountain: -8 hours, US Pacific: -9 hours, Japan: +8 hours)

Below are some details on the community experiments and conference agenda. In particular, see the link below to submit your recommendations

1. Community experiment: The centerpiece of our conference will be a community experiment on delta formation and stratigraphy in the laboratory of Joris Eggenhuisen at Utrecht University. We encourage you to review the description of the community experiments here. Variables for the community experiments will be proposed by participants! Please submit your recommendations for the community experiment by Google Docs here, by Friday, Oct. 24. 
2. Workshop agenda: Each day of the main workshop (Tues-Thurs) will be built around a theme for the sediment experimental lifecycle and will include presentations by keynote speakers, observation and analysis of community experiments, and discussion of data management practices. On Friday, we will then be convening focused discussions to help push SEN projects forward through the upcoming year. You can view the draft workshop agenda here.

Best Regards,

Raleigh Martin, Kim Miller, Leslie Hsu, Wonsuck Kim, and Brandon McElroy

Sediment Experimentalist Network: SIESD Report and a New Year

Dear Sediment Experimentalists,

SEN had a great time at the Summer Institute for Earth Surface Dynamics last month, but now summer is over and it's time to introduce SEN to new students and colleagues. We're excited to share new information and resources with you in Year 2 of SEN.

1. Summer Institute for Earth Surface Dynamics 2014
2. Recruit new lab members and colleagues to SEN
3. Our growing SEN Knowledge Base

Summer Institute for Earth Surface Dynamics 2014

SEN gave a talk at the Summer Institute for Earth Surface Dynamics, "Sediment Experimentalist Network (SEN): Sharing and reusing methods and data in Earth surface process experiments."

• View the slides on slideshare
• See photos from SIESD's experiment day

Recruit new lab members and colleagues to SEN

Do you have new group mates who are about to embark on a sediment experiment adventure? Have them join the network and receive news and updates related to sediment experimentalist research.

• Sign up for SEN news

Our growing SEN Knowledge Base

The SEN Knowledge Base is being populated with wiki articles to help you conduct your research. The articles document examples of experimental methods that you can use and modify. Check out two new entries related to the SIESD 2014 experiment:

• Still image correction set up
• Setting up an IP camera to live stream experiments

Stay in touch and always let us know how we can help.

Happy experimenting,
The SEN Team
sedimentexp@gmail.com

--
Help us grow our network and forward this link to a colleague: Sign up to join the SEN Network

--
Sediment Experimentalist Network
Blog: http://sedimentexperiments.blogspot.com/
Website: http://workspace.earthcube.org/sen
Twitter: http://www.twitter.com/sedimentexp

Sediment Experimentalist Network July News and Tools

Dear Sediment Experimentalists,

SEN was at the EarthCube All Hands Meeting in Washington, D.C. recently, where we met participants from other Research Coordination Networks and EarthCube Building Block projects.

We are sharing a few things we discovered that may be useful to you:

1. ESIP data management course
2. Ten simple rules for the care and feeding of data
3. EarthCube All Hands call to action
4. Reminder: Data Management Plan Tools

ESIP data management course

At the Education breakout we were reminded about the ESIP Data Management Course, brought to you by Earth Science Information Partners - with downloadable modules (slides or movies) about data management topics like “Advertising your data”, “Backing up your data”, and “Building understandable spreadsheets”. These can be referenced in your data management plans.

Ten simples rules for the care and feeding of data paper 

In another EarthCube breakout session we discovered a paper with good advice on how to treat data, and give suggestions for linking data to publications, publishing code, and stating how to get credit.
Ten Simple Rules for the Care and Feeding of Scientific Data, doi:10.1371/journal.pcbi.1003542

EarthCube All Hands call to action

EarthCube is currently soliciting any interested people to help shape the future direction of EarthCube. The viewpoint of scientists and practitioners is particularly needed. Those that participate will shape many of the decision, funding, and communication practices. Click here for more information and to express your interest in becoming a member of the Science Committee, Tech/Architecture Committee, Engagement Team, Liaisons Team, and the Leadership Council. Membership is open to all interested persons. There will be webinars on July 17 and 21 with more information. You can also email Leslie or Raleigh if you have any questions about this.

Data Management Plan Tools

For those of you preparing proposals now, we remind you of two popular Data Management Plan Tools to help you build a plan with all of the important components.

• IEDA Data Management Plan Tool
• CDL Data Management Plan Tool

Stay in touch and always let us know how we can help.

Happy experimenting,
The SEN Team
sedimentexp@gmail.com

--
Help us grow our network and forward this link to a colleague: Sign up to join the SEN Network

Sediment Experimentalist Network Homepage

SIESD 2014 Summer Institute on Earth-surface Dynamics: Complexity and Predictability in Depositional Systems

Complexity and Predictability in Depositional Systems

The National Center for Earth-surface Dynamics is proud to provide ongoing support for the 6th  annual Summer Institute for Earth-surface Dynamics. The SIESD engages graduate students and young researchers in interdisciplinary investigation of Earth-surface processes based on integration of theory, physical experiments, field work and numerical modeling. This year’s theme builds on the SIESD 2013 theme of linking surface processes and depositional records, with a new focus on formal, quantitative analysis of complexity and its effect on prediction both of evolution and change in present-day systems and of 3D structure in the subsurface. The key objective in this year’s SIESD is to develop a working knowledge of analysis tools that can help us navigate the complexity of surface-process interactions to provide insights into the behavior of depositional systems.

Participant costs (enrollment, accommodation, and on-site meals) are supported by NCED. Students will be responsible for the cost of transportation to and from Minnesota and for all incidental expenses.

Dates and Location:
August 12-21, 2014 Minneapolis, MN

Eligibility:
The Summer Institute is directed towards graduate students in the final years of their PhD program, postdocs, or early career scientists (three years from PhD). Applications from women, minorities and individuals with disabilities are strongly encouraged.

Application Procedure:
Online application and instructions are available at: nced.umn.edu/siesd Applica-
tions are open now. Notification of placement will be announced June 2014.

Application Deadline:
June 20, 2014

Contact:
Deb Pierzina (Email: pierz001@umn.edu)

For more information:
nced.umn.edu/siesd

The 6th Annual SIESD is organized by the National Center for Earth-surface Dynamics, a National Science Foundation Science and Technology Center funded by the Office of Integrated Activities under agreement EAR-1020914

Sediment Experimentalist Network:SEN this Summer

Dear Sediment Experimentalists,

It’s almost summer, and almost the one year anniversary of SEN. Sediment Experimentalist Network officially started on August 1, 2013. In this newsletter we review what’s happened this past year and what’s coming up, including some goals before we get to the one year anniversary. Make SEN part of your summer!

1. Year 1 Activities and Report
2. How you can participate this summer
3. Experimental Collaboratories
4. What’s new with EarthCube

wordle from our community-created SEN sediment resource list

1. Year 1 Activities and Report
We held a virtual meeting of our steering committee in April, you can view our Year 1 Report slides, which review our workshops and resources, and give a preview of our future activities.

2. How you can participate this summer
SEN will be active this summer recruiting content for our shared resources, and aiming to hit our goals before the August 1 anniversary. Contact us at sedimentexp@gmail.com if you have some time this summer (anything from 15 minutes to days) and want to learn how to help.

• Sediment and Instrument Resource List: We (and that means you, our readers) have compiled 33 vendors for sediment and 28 vendors for instruments -- take a look, add your own resources, and share with your lab mates. We want to grow this list before our 1 year anniversary.
• SEN Data Catalog:  *Now open for beta-testers*, check it out as a way to promote your research and/or fulfill that data management plan requirement. Contact us with any questions.
• SEN Wiki for Experiments:  Want to find an instrument that will work for your experimental method, see how others have tackled a problem, or just see what new research is happening? The SEN Wiki is now open and we need contributors. Contact us with any questions.
• Forward this email to a colleague and tell them to join on our SEN sign-up page.

3. Experimental Collaboratories
SEN-EC, Experimental Collaboratories, has kicked off with University of Texas, Austin, and University of Wyoming sharing a live-streamed experiment. We'll be growing the network of labs with the capability to stream experiments over the lifetime of SEN, but anyone with an internet connection can always join. We will be announcing future collaboratories soon, Contact us to learn more.

4. What’s new with EarthCube
SEN is part of EarthCube and will be participating in the EarthCube All-Hands meeting, where we'll report on our network-building activities and collaborate with technical teams that are building tools to help you do your science. EarthCube is setting up its governance structure and desires your feedback, see the charter review page if you want to learn more and contribute your voice. We hope that SEN is your pathway to EarthCube - let us know any questions you have.

Coming soon:
- Answering questions about data management plans
- Describing your experiments and data for reuse
- Promoting your papers and data to your peers

Drop us a line telling us what SEN can do for you.

Happy experimenting,
The SEN Team
sedimentexp@gmail.com

Sediment Experimentalist Network March 2014 News

Dear Sediment Experimentalists,

Here's the March round-up. Contact us at any time with comments or ideas.

1. SEN Knowledge Base
2. Sediment and Instrument Resources List
3. Help us build our network

1. SEN Knowledge Base
The SEN Knowledge Base (SEN-KB), soon to be beta-launched (early April), is a web-based resource containing both (1) a "Data Repository" with metadata and links to datasets for experimental sedimentology research and (2) a "Wiki" with useful information about experimental setups, methods, equipment, etc.  Both are designed to grow collaboratively with user input.  We need You to be a beta tester, contact us at sedimentexp@gmail.com.

Our old Fusion Table has been recast into a new Data Catalog with improved search and display capabilities.

2. Sediment and Instrument Resources List
Ever wonder where is the best place to find a certain size of sediment or a very specific instrument? Look no further.  We are compiling a resource list (http://goo.gl/NUA5mS) for users to share their knowledge about vendors for both typical and unusual items.  The list is open to all, please contribute!

Resources like this are built by first consulting our SEN Discussion List. The previous resource developed was a compilation of video-sharing options.

3. Help us build our Network
Do you know a Sediment Experimentalist in your lab or another that is not receiving these newsletters? Send them to the sign-up page so that they can stay informed with the latest SEN news. We need your help to grow our network, especially with new incoming graduate students who can benefit from the shared knowledge.

Happy experimenting!
SEN

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Sediment Experimentalist Network

Blog: http://sedimentexperiments.blogspot.com/

Website: http://workspace.earthcube.org/sen

Twitter: http://www.twitter.com/sedimentexp

Sediment Experimentalists February 2014 News

1. SEN and Recent EarthCube Activities
2. Sharing video files of experiments
3. Opportunities to collaborate with new projects

1. SEN and Recent EarthCube Activities

SEN is partially funded through the NSF EarthCube initiative, so we participate in EarthCube activities, bringing sediment to cyberinfrastructure (or vice versa). Here are some recent activities:

Funded proposals workshop:

From February 12-14, SEN attended the EarthCube Funded Project (Portfolio) Assembly Workshop. SEN is one of three RCNs (Research Coordination Networks) funded in the first round of EarthCube funding. At the workshop, we looked for synergies and conflicts with other EarthCube projects, some examples of some neat opportunities are listed below!

CINERGI list

The CINERGI project is building an inventory of resources to “meet the challenge of finding resources and information across disciplines”. We are compiling a list of SEN-related resources,  many from previous SEN surveys and questionnaires, for presentation to you. (What is a resource? Almost anything - webpage, software, blog, twitter feed, database.) Anyone can add a resource! If you are interested in helping to build our community inventory, email sedimentexp@gmail.com.

Field Trip to Yosemite and Owens Valley

The Earth-Centered Communication for Cyberinfrastructure (EC3) project is organizing a field trip to Yosemite and Owens Valley to foster communication between field geologists and computer and cognitive scientists. EC3 recognizes that communication between field scientists and experimentalists is also of great importance, and invites applications to the trip (mention that you are involved with the SEN RCN). Read more about the field trip and apply to attend by March 10, 2014!

End User Communities & Professional Societies Assembly Workshop

March 18-20 in Washington D.C. The goal of this workshop is to facilitate communication, collaboration, and coordination among the scientific and technical professional societies whose membership includes people engaged with geoscience communities. Are you interested in learning more about EarthCube? Registration is open to the public, read more...

2. Sharing video files of experiments

We recently started a Sediment Experimentalists Discussion Listserv. We hope you will Join the Listserv! You can see a write-up about video sharing from the discussion list at:

http://sedimentexperiments.blogspot.com/2014/02/sharing-video-files-of-experiments.html

3. Opportunities to collaborate with new projects

Here are two opportunities to participate in new projects in the second round of EarthCube awards. Please contact Anne or Albert (emails below) if you’d like to join their efforts. 

Participate in a Model-data comparison tool project for the Geosciences

Greetings! My name is Anne Thessen and my colleagues and I are working on a proposal for the EarthCube Amendment III solicitation due March 12. The proposed work is to build a tool for comparing model-output with field data and was originally created for oceanographic applications. We want to make it more robust and capable of serving more communities. The tool would work by iterating over data points in model output and finding its nearest-neighbor in the field data based on space/time. The output would be a data table connecting specific points for input into statistics or visualization software. In order to make the tool useful for different disciplines, we need testers from many communities to try the software and give feedback. We anticipate testing sessions of 30 min maximum every 2-3 months for the duration of the 2 yr project. We would really appreciate it if some of you would be able to test the software and let us know what you think. If you are interested in participating, please email me at annethessen@gmail.com. We would like to be able to get a letter of collaboration for the proposal.

Thank you.

Participate in inland-waters RCN

The EarthCube 'inland-water bio-geochemistry and fluvial sedimentology' (C4I) community is about to submit a RCN proposal (03/12/14; PIs: Emilio Mayorga, Alba Argerich, Basil Gomez, Bernhard Peucker-Ehrenbrink, Albert Kettner). Therefore we want to reach out to the experimentalists community to seek potential participation. As all EarthCube RCNs this is about data, metadata, standards, cyberinfrastructure needs for now and in the future to advance science, etc, but in the light of inland-waters. Any cross-breading between the communities will stimulate learning from each-other experiences. If you are interested, don't wait, please send an email to albert.kettner@colorado.edu with just "SEN-RCN: yes keep me informed about inland-water RCN" as subject; it only takes 10 seconds! Given that the project will be funded, we'll add you on our mailing list. Thank you!, Albert.

***

Happy experimenting,

The Sediment Experimentalist Network

http://workspace.earthcube.org/sen

Sharing video files of experiments

This post is a summary of responses to a video-sharing inquiry on the SEN Discussion List. Join and participate in Q&A about sediment experiments!

Here are some options for a wide range of video-sharing needs - from small to large files, from private to public sharing, from local hardware to cloud services, and from free to paid… This information might be good to keep in mind when planning or budgeting for new projects. Further comments extremely welcome, especially if you’ve had good or bad experiences with any of these platforms.

Review of the problem:

Large number of large size videos to share privately among a dispersed working group.

The winner: QNAP NAS RAID and Multimedia Library

Pro: LOTS of storage. Easy file sharing. Log-ins. Can share any file format.

Con: Requires some $$ and some set-up.

If I were setting up a lab right now, I’d use some start-up up funds to purchase a QNAP NAS (Network-attached storage). If I were writing a proposal, I’d write it in for data storage. 

I’m far from an expert, but a QNAP 22Tb RAID6 (32Tb raw) just arrived at the Columbia Granular Group. (Read wikipedia’s article about RAID, “redundant array of inexpensive disks”.) In addition to abundant storage for a reasonable price, it comes with extremely easy-to-use firmware for file sharing, a video station, and apps (sync with Google Drive or Dropbox).

With log-in accounts and a logical folder structure that is agreed upon by the group, all group members will be able to access and download what they need. Our humongous raw video files will probably be converted to a standard format like .mp4, then stored in a parallel file structure for browsing. This was the best option for the large volume, easy access, privately-shared video issue that initiated this post. 

Other options:

This is not an exhaustive list, but rather some interesting points I just learned from your recommendations and researching the video-sharing question.

Vimeo

Pro: Several levels of membership for different storage volumes, privacy settings.

Although I had seen videos shared on vimeo before, I wasn’t aware of their membership level details. Memberships are determined by the volume of video per week. Basic (free) is 500 MB per week. Plus ($60 per year) is 5 GB per week, and PRO ($200 per year) is 20 GB per week. Those numbers can add up quickly to give you a large amount of storage per year.

There are no file size restrictions and the videos can be as long as you like. This seems like a good platform for sharing videos to illustrate results (better than just posting the link on a personal website).

Flickr

Pro: Lots of free space, 1 Tb free

Con: Limit of 90 second videos, since it is primarily a photo-sharing site

If you already use Flickr, you may want to take advantage of its generous storage space to share short videos. Flickr video FAQ.

YouTube

Pro: privacy settings, linked to Google (if you like that kind of thing), live streaming (live experiments!)

Con: ads, high probability of being distracted by suggested videos

More academic projects are starting to use YouTube channels as video sharing sites. By clicking a few buttons, you extend the basic account to share videos longer than 15 minutes, and stream live events. There’s integration with a Google account and Google+, if you already have an account set up for your project.

Figshare

Pro: store, share, discover, cite, and on a site specifically for researchers

You may want to check out the figshare post "A YouTube for Scientists". Another option for sharing video (in a citable way!). 

***

Hope to see lots of SEN videos in the future!
Leslie

SEN January 2014 News

Dear Sediment Experimentalists,

The new year and new semester are in full swing. Take a look at some of our new resources and join the discussion listserv so we can start some Q&A about experiment and data management procedures.

Sedimentary Record Articles: SEN’s motivation and early activities are summarized in an article in the recent December 2013 issue of The Sedimentary Record. The issue also has a experimentally-relevant piece on NCED2. Click to read the article...

Visit the new SEN EarthCube Workspace: SEN is funded partially through the NSF EarthCube initiative and we have a SEN page on the EarthCube workspace to show our activities. You can see descriptions of other funded EarthCube projects at workspace.earthcube.org.

We need SEN Knowledge Base Testers: We’re working to get out the first beta version of the Knowledge base and have been testing it with the SEN Fusion Table entries. If you would like to be a beta tester, contact us at sedimentexp@gmail.com.

Join the SEN Listserv: Have a question about experimental procedures or data management and don’t know who to ask? Join our listserv for active discussions on topics for sediment experimentalists. We expect more email traffic on this list than on the newsletter mailing list, so we’ll let you to opt in. The address to post to the list is sedimentexp@earthcube.org.
Register at: http://mail.earthcube.org/mailman/listinfo/sedimentexp_earthcube.org