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Use Case: DCMIP 2012

Authors: Sylvia Murphy, Cecelia DeLuca, Christiane Jablonowski

Summary: A group workspace is used to coordinate a two-week summer colloquium that centers on a Model Intercomparison Project (MIP), and serves as a vehicle for distributed, collaborative data analysis. The two coordinators of the MIP and a technical coordinator are all located at different institutions. The colloquium itself will be held at another institution, the Modeling Center. Participants include about 50 graduate students and researchers, and a number of invited speakers are giving plenary talks. 10 different modeling groups are represented, and each of these has a lead. There are a number of local support staff from the Modeling Center assigned to each modeling group that's participating. The workspace is created as part of a gateway that can also archive and disseminate the data from the MIP.

PHASE 1: PREPARATION

Action: Coordinator1 goes into the workspace to set things up before the colloquium starts. She creates a project and defines who will have access to the data produced at the workshop. She plans to make the data archive public only after it has been quality checked [It was decided later to make the archive public from the beginning]. She makes herself, Coordinator2 and a technical assistant administrators for the project.

Requirement Action Log
Create and name a project workspace.
  • We created the concept of projects in CoG.  DCMIP set up 3 and linked them together.
  • Release 0.1
Be able to define a set of administrators for the workspace.
  • We created an administrative role with the ability to modify the project, to accept members, and to assign roles.
  • Release:0.3
Be able to password protect the data and therefor limit access to those with the group password.
  • Not done: It was decided to make the data public
  • Ticket:  140


Action: Coordinator1 then adds a description of the MIP to the project workspace. Coordinator2 adds the program schedule for the colloquium. The technical assistant adds contact information for both coordinators and himself.

Requirement Action log
Be able to add content to the project
  • We did this through the ability to create wiki pages and link them through a navigation bar on the left.  Originally we thought this would be done through project-level MIP metadata, which is how the original requirement read ("Workspaces should have project metadata that can be filled in by the administrators.)
  • Release 0.1
Be able to make information limited in visibility to a group.
  • We did this by making pages able to be private and visible to only group members.
  • Release 0.6


Action: Coordinator1 uploads 5 scientific papers that are general references for the colloquium. Coordinator2 uploads a document that explains the rationale for the experimental test cases and how they should be configured.

Requirement Action Log
Administrators and selected group members should be able to upload PDF, TEXT, or other document types to the workspace so that everyone has access to the documents and can view or download them.
  • We did this by adding a general document upload capability.  Documents can be uploaded to a particular wiki page or to the project as a whole.  Project members can view all the documents that have been uploaded to a project.
  • Release


Action: Coordinator1 then uploads two figures that will be used as examples for the types of figures she wants participants to produce. She creates a metadata caption for each figure.

 

Requirement Action Log
Upload figures to the project
  • We created a general figure upload capability.  Figures can then be imbedded into a wiki page using the wiki widget
  • Release:
Be able to caption a figure
  • While we originally thought this would be a metadata caption, we ended up just using the wiki to add a caption to a figure.
  • Release 0.1
Be able to embed images with captions in the workspace.
  • We did this through wiki pages
  • Release 0.1


Action: Coordinator2 then does a search on datasets already archived by [data node attached to the workspace].  She picks out 5 datasets she wants the participants to use and saves links to them in the group workspace.  She also saves links to metadata from the search to the project workspace.

 

Requirement Action Log
Be able to save links to data from data search to the project workspace.
  • This was done by enabling results from teh data search to be saved as a project bookmark.
  • Release 0.5
Be able to save links to the metadata from the metadata search to the project workspace
  • Not done in time for DCMIP 2012.  No metadata search was created.  Manual links were imbedded on modeling group pages instead.

Action: The instructor then decides she wants to add a link to the American Meteorological Society meeting on the MIP workspace because she wants participants to know about a special session there related to the MIP.

 

Requirement Action Log
Be able to add a link to the group workspace within a comment or separately.
  • The chosen wiki had this capability
  • Release 0.1


Action: Coordinator1 goes to a discussion area and posts an initial question that she wants all the participants to answer: "What do you hope to get out of this colloquium". She sees her identity indicated on the initial post. The conversation must stay permanent, and all users of the MIP workspace must be able to see it.

 

Requirement Action Log
Create an interactive discussion area.
  • There were two approaches to this.  The ability to comment on pages and the addition of notes to bookmarks.  Identity is recorded through the "last update" comment.


PHASE 2: THE PARTICIPANTS ARRIVE

Action: Participants all register for the portal that houses the MIP workspace (some were already registered and did not need to) and create unique user names, passwords, and public names, which may have nothing to do with their real name. With registration, each participant gets a personal workspace and an optional profile in the portal. Profiles can include: pictures, areas of interest, and contact information. All of the modeling groups leads fill out this information and make it visible to the MIP project. Many of the students fill out this information and make it visible globally throughout the portal.

Requirement Action Log
Create a user registration process
  • Registrants must provide some basic information.  They choose their own user name and password.  Their user name is public.
  • Release 0.2
Create public user profiles like social networking sites have
  • NOT DONE for DCMIP 2012


Action: The technical assistant collects public names from participants and approves their membership in the MIP project group. He gives read and write permission for the group workspace to the invited speakers and researchers, and read permission to students. This prevents students from changing the structure of the group workspace, but still lets them contribute posts in the communication area. The MIP project appears in each participant's individual workspace as one of the projects in a list of projects that they are participants in. The technical assistant finds out someone he thought was a student is actually a speaker and changes their permissions.

 

Requirement Action Log
Administrator approves project membership
  • Administrators were given a link on the left nav bar that says "List Pending Users".  They get an email when someone requests membership and can accept using this link.
Administrator sets and can change the roles of project members so that some have read only access.
  • It was decided to only have two roles (Admins and Group Members).  Everyone can edit everything within a project they belong to.  After the fact, Administrators can change roles using the "List of Current Users" interface
Create personal workspaces
  • NOT DONE:  It was decided not to create individual workspaces


Action: The participants go to the discussion area and post their replies to Coordinator1.

Requirement Action Log
Be able to participate in a discussion
  • Discussions occurred on wiki pages
  • Release 0.1


Action: The leads for each modeling group create workspaces in the portal for their model and define them as being part of the main MIP workspace. They add information about which room they will be located in for hands-on sessions, who is assigned to them as technical support staff at the Modeling Center, and which students are included in their modeling group.

Requirement Action Log
The ability to create child projects and link them to parent projects.
  • For the workshop, they used pages for each modeling group vice sub-projects
  • Release 0.4


Action: The leads for each participating group go to a GUI where they can enter in metadata about the runs. Coordinator1 has chosen in advance what metadata she wants collected, and the interface enforces a controlled vocabulary for some questions and free text for others. The metadata is automatically uploaded into the MIP workspace in the portal.

Requirement Action Log
An online means of creating trackback metadata that can accommodate controlled vocabularies as well as free text.
  • Implemented the esdoc autogenerated questionnaire that was customized specificially for DCMIP 2012



PHASE 3: DURING THE MIP

Action: Coordinator1 views a table of runs and their status. The table shows which runs have been completed and have submitted data. Metadata associated with each run identifies which test each run is associated with, and includes information such as resolution.

Requirement Action Log
Abilitity to publish data
  • Luca ended up running the publishing process.  The group put their data on a server at NCAR and then once a day it was automatically transfered to NOAA.  Luca then manually published the data to the ESGF data node.
Ability to view data metadata
  • Luca created a link to the data metadata from the ESGF node
The ability to determine which data and metadata is expected to be collected for a particular MIP, and to present which experiments have data available in a table.
  • This was created manually


Action: One of the participants completes his run and now wants to visualize his data. He clicks on a visualization tab and is able to create several plots of his data using an interactive GUI. He is able to apply the same visualization directive to multiple runs, producing several plots at once. He then uploads the plots to his personal workspace, a data analysis blog in the group workspace, and also to the pages displaying the simulation metadata.

Requirement Action Log
Produce images from datasets
  • LAS comes bundled with the ESGF node attached to CoG.  This tool was used to create images.  LAS requires the data to be in a certain format. Often the modeling groups would not reformat their data, making LAS impossible to use.
Apply the same visualization directives to multiple datasets
  • Ditto
Be able to upload images created by the visualization package to the workspace
  • It was hoped that LAS would create a "save to CoG" feature so that images could be directly saved.  This is not happen.  Instead, users saved images locally and uploaded them to the workspace.
Be able to upload images to the pages that display simulation metadata
  • Not done in time for DCMIP 2012


Action: Another participant creates a python script that she uses on her own laptop to create EOFs of some of the model output data. She posts this script so that others can use it too.

 

Requirement Action Log
Be able to upload scripts Release 0.1


PHASE 4: FINALIZING THE MIP

Action: All of the runs have been done. Coordinator2 asks the participants to examine the effects of resolution on results. The participants go into the metadata comparison tool and select a few runs they might want to compare along with the metadata they will use to help them narrow their selection. They hit submit in the online GUI and a table of the metadata across the chosen runs is displayed. The metadata in the comparison table includes thumbnails of visualizations for some of the simulations, which can be enlarged by clicking on them. Participants do this several times until they decide on the runs that interest them the most.

Action: Next the participants go into the visualization tool again. They each select a set of runs and produce a overlay comparison plot. They save several plots to their personal workspaces while they are working. Each participating modeling group in the MIP selects one plot and posts it to the discussion area, and describes why those runs interest them and what they have learned scientifically from the comparison. Other participants engage them in the discussion area in a scientific debate.

Requirement Action Log
Compare metadata by selecting simulations and attributes, including visual results
  • Were going to use the esdoc comparison plugin.
  • plugin not available in time for DCMIP 2012
Be able to compare model runs and discuss the results
  • Completed using a 3rd party visualization tool
Create overlay plots and other comparative graphics.
  •  Completed using a 3rd party visualization tool
Save images to personal workspaces from the visualization tool.
  •  No personal workspaces were created
Be able to upload images to the discussion area and start a thread about them.
  • Completed by using the wiki
  • Release 0.1


Action: Coordinator2 examines a couple of sample datasets. She notices that the data has some errors. She examines how the model was run, makes some changes to the configuration and reruns the simulation. She then checks to see if the new data has replaced the old in the data archive.

Requirement Action Log
Be able to determine the version of datasets
  •  Completed via the ESGF node
Be able to update datasets
  •  Completed via the ESGF node
Be able to update metadata
  •  Completed by updating the esdoc questionnaire

 

Last Update: Nov. 5, 2014, 2:45 p.m. by deleted user