Frequently Asked Questions
Below are answers to some frequently asked questions submitted to the GCE IM office by GCE investigators and students. Click on the question hyperlink to view the answer, or click on the "Show/Hide All Answers" link above to display all answers at once. This list will be updated frequently, with new Q&A included in the weekly GCE Newsletter email. Also see the GCE Information System Guide for a more in depth list of GCE Information Management topics.
Question: "My journal requires that my data be archived and cited with a DOI before publication - what do I do?"
Many journals now expect authors to make the data underlying published articles available online, and some make this a strict requirement before publication (e.g. see ESA's data policy at http://esapubs.org/esapubs/DataReg.htm). The LTER Network has partnered with EZID at Purdue to provide stable DOIs (digital object identifiers) for data sets published in the LTER Data Portal to help LTER sites meet these requirements.
All public data sets in the GCE Data Catalog are regularly synchronized to the LTER Data Portal, and the DOIs and data set citations are retrieved and displayed on GCE Data Set Summary pages (see figure). So all that you need to do is contribute your data to the GCE IM Office as usual, and make sure to specify a public release date that coincides with the submission date or final publication of your manuscript, as appropriate. We will then publish your data in the LTER Data Portal on the specified date and provide a DOI and citation you can relay to the publisher. Note that we cannot currently provide DOIs for private data sets, so contact the IM Office to discuss strategies for dealing with citations for sensitive data.
Question: "Can I archive data in the GCE Data Catalog and get a DOI if the research was funded entirely by another grant?"
This is a complex issue that generally requires discussion and negotation, so investigators are urged to contact the IM Office well in advance, ideally when writing the data management plan for the proposal. The GCE Executive Committee has not come up with hard-and-fast criteria for archiving non-GCE-funded data in our infrastructure, but factors that will be considered are participation of GCE personnel, how closely-aligned the study is to GCE research goals, and the value of the data for comparison with GCE study data.
If approved, investigators will need to provide complete details about the funding source (granting agency, grant number, PIs, abstract, study dates, etc.) in addition to all other information requested on the GCE Data Submission form. If extensive post-processing or metadata generation are required, or if large data files are involved (>1 GB), then resources may be requested to offset GCE costs in archiving and hosting the data.
Non-GCE data will be displayed in the catalog alongside GCE data sets, but will include "OTH" (other project) in the accession and appropriate grant attribution information in both text and EML metadata, listing GCE as the publisher and co-contributor of the data but not the funding project. For an example, see data set PLT-OTH-1509 from a recent Chinese study on invasive Spartina alterniflora that Steve Pennings participated in.
Yes. Investigators and students can view a data submissions report on the private GCE website, listing the status and citation information for every data set on which they are listed (see figure). Here's the link to the report page: https://gce-lter.marsci.uga.edu/private/app/datasets.asp. Note that the report is automatically keyed to your GCE website login, and the link is also available on website menus under Private Site > User Information > View Data Submissions.
Question: "We need to connect a computer to a piece of outdoor field equipment. What should we use?"
As environmental sensor systems and instrument packages become more sophisticated, it's common for them to require full-time tethering to a computer system for operation rather than a simple data logger. When the instrumentation is installed near a laboratory building or other enclosed structure with climate control and power, the simplest (and cheapest) solution is often to connect the instrument to an indoor desktop or laptop computer via physical cable (up to 30m), or a wireless serial or Ethernet link (up to 3000m). Here's information about an affordable long-distance WiFi serial adapter that can be used to wirelessly connect an instrument to a computer located over a kilometer away if no obstructions are present: http://www.usconverters.com/wireless-rs232-adapter-ez500. Wireless serial adapters operate transparently, so once the connection is made the computer and instrument operate just as if a physical serial cable is attached and no special software or drivers are required.
When the instrument is deployed in a more remote location, or heavy tree cover limits wireless range, then the situation rapidly becomes more complex ... and more expensive. Standard desktop and laptop computers don't fare well in the moist, salty air around Sapelo, causing ports, fans and other exposed parts to corrode quickly. And if the computer is placed in a waterproof enclosure to protect against the elements it will rapidly overheat due to active cooling requirements. In addition, desktop and laptop power supplies are not well suited for variable input voltage from the solar battery systems often used to power remote instrumentation. Considering these risks, a much better solution is to use a waterproof industrial PC actually designed for outdoor conditions, such as those sold by SmallPC.com.
For example, we purchased a SmallPC SC240ML waterproof computer in 2012 to establish a wireless data hub at Marsh Landing for the GCE Flux Tower and future instrument deployments nearby (e.g. ADCP, SeapHOx). This computer is installed in an open storage room at the end of the pier (see photo) and it has operated flawlessly in all weather conditions for over 3 years, acquiring and transmitting >300 MB of data per day to servers at UGA via 900 MHz and 4G cellular links. We also recently purchased a more compact version, the SC215ML "iBrick", for temporary outdoor installations such as the Ceilometer and SODAR used by the LeClerc lab for atmospheric studies on Sapelo. Although not cheap at $1500-$2500 each (depending on configuration), these rugged waterproof computers are ideally suited for long-term outdoor use and will avoid the headaches (and associated data loss) of re-purposing a standard computer or laptop for this task.
(contact Wade Sheldon for additional information)
Question: "Can we include detailed protocols in our data set documentation without pasting all the text into the data submission template?"
Ecological Metadata Language (EML), the metadata standard adopted by the LTER Network and used at GCE, does support including links to protocols when documenting data set methodology. Protocols define abstract, prescriptive procedures for generating or processing data (i.e. standardized methods). In order to support this feature, the GCE Metabase Metadata Management System has now been extended so protocol documents can be linked to methods steps in data set metadata. The web links and descriptions of protocols will also be included in EML metadata submitted to the LTER Data Portal and DataONE for long-term archiving.
Investigators are still encouraged to provide detailed descriptions of what work was actually done when collecting samples, performing analyses and processing their data in the 'Method Steps' fields of the template. However, if you used published standard methods or your lab has developed a detailed protocol that was followed those protocols documents can now be referenced and linked to provide more detail to future data users without cutting and pasting the text.
To provide protocol information for your data sets, please use the updated Data Submission Template (dated Mar 2016) and fill in descriptions and links to the protocol documents on the new 'Protocol' worksheet. Also make sure to make a note in the 'Protocol' column of the corresponding 'Method Step' on the 'Documentation' worksheet. If the documents are already available online at a stable URL (e.g. USGS standard methods) you can just provide the link in the data submission template. Otherwise, please upload a copy of the protocol document(s) in text, Microsoft Word or Acrobat PDF format along with your completed template when submitting your data to the IM Office. Protocol documents will be archived in the GCE File Archive under the Documents/Procedures/Protocols section to provide a stable URL and file versioning, and then linked to the corresponding methods in your data set.
Note that the same protocol document or link can be associated with any number of data sets or methods steps, so if you have already submitted your protocol along with a previous data set you can just refer to the link in the GCE File Archive. As always, please contact Adam Sapp or Wade Sheldon with any questions about the data or metadata submission process.
The computer software used to process and analyze environmental data is increasingly being recognized as a critical part of the data provenance, and having access to the specific software used can be critical for scientific reproducibility. This is particularly true if custom scripts were developed using R, MATLAB or another language for the analysis.
The GCE Metabase fully supports archiving supporting files, such as software code, photographic imagery, maps or other resources, along with conventional tabular and GIS data files. These support files can be described on the 'Non-Tabular Data' worksheet in the Data Submission Template then uploaded along with the data files. Links and descriptions of these files will be displayed in data set summary pages of the GCE Data Catalog under Downloads, and the files will be included when data sets are archived in the LTER Network Portal and DataONE.
Note that if proprietary or commercial software were used the code should not be submitted to avoid copyright violations. Instead, document the name and version details of the software used and provide a web link (if applicable) in the methods metadata instead. Also, if many individual scripts or libraries were used please package them into a single Zip archive before uploading.
(contact Wade Sheldon for additional information)
Question: "How do I get a private site login for my new student or staff member so they can fill out a research request form"
The best way to request a login is to email the GCE Information Management Office (firstname.lastname@example.org) with your request and cc your student or staff member on that email for follow-up. To expedite the process, please provide information about the person's role in your lab and degree program (for students) to aid IM staff in filling in the personnel database record. A login and provisional password will be emailed to them, and they will also be signed up for relevant GCE email lists at the same time.
Note that per project bylaws, access to the private GCE-LTER website is restricted to active PI's and Affiliated Professionals/Investigators and their current staff and students. Research collaborators, visiting scientists and students from other labs temporarily working with you on Sapelo do not qualify as GCE members, and should be directed to SINERR's research request form for permission to conduct their studies under SINERR, UGAMI or Georgia DNR sponshorship, as appropriate.
Next steps after approval vary depending on the nature of the research being conducted. For short term (under 24 hour) or observational studies that do not involve equipment installation, collections or marsh impacts, GCE approval is typically all that is required. However, studies that involve longer-term equipment deployments (>24 hour) or will impact the marsh ecosystem often require a Letter of Permission (LOP) or Permit from the Georgia DNR Coastal Resources Division or other permit authority.
After your application is reviewed and approved you should receive an email with a link to a Permits web page (see screenshot below) that contains personalized instructions based on the nature of the proposed work. If your study will likely require a DNR LOP, instructions and links will be provided for downloading a pre-signed Revocable License form and saving your completed application in PDF format for emailing to CRD. If you didn't keep the email or need to return to this page, you can also access it by clicking on the "Permits" link under "Tasks" at https://gce-lter.marsci.uga.edu/private/registration/view_requests.asp (note that if no "Permits" link appears, your application does not require a formal LOP and you're done). We also ask that you return to this page and upload a PDF version of any LOPs or permits that you obtain for our records.
Please note that individual investigators are ultimately responsible for obtaining all necessary permissions and permits from cognizant state and federal authorities (e.g. SINERR, Georgia DNR, FWS, USCG and Army Corps of Engineers), and GCE can only play a facilitatory role in this process. Obtaining permission to do research on Sapelo is an ever-evolving process, so please plan ahead and ask questions early in the process to avoid complications and delays in starting your research.
(contact Wade Sheldon for additional information)
This material is based upon work supported by the National Science Foundation under grants OCE-9982133, OCE-0620959 and OCE-1237140. Any opinions, findings, conclusions, or recommendations expressed in the material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.