GenSpace

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Contents


Features and Requirements

  • Features
    • Description
      • Use Cases/Things to do


  • Ontology
    • Use domain knowledge (through config files of ontology) to group tools
      • Data mining using rollups for other use cases (e.g. suggest a user to use "network clustering" tool rather than tool A)
      • Show window to user showing hierarchy of tools in the ontology
  • Online Help
    • Provide documentation for usage and help through geworkbench
  • Workspace/File Sharing
    • This can be used by users to share their files and workspaces with other users
      • Need to investigate more in detail especially with respect to to security/privacy issues
  • Statistics
    • Provide detailed statistics on geworkbench usage
      • Admin Section and (maybe) users can see what tools are used the most in a group, overall, etc.
  • User Study on geWorkbench
    • How does geWorkbench fit into the ideal bioinformatics workflow?
      • Find "Expert" researchers (ex, people who do a lot of research, not necessarily with geWorkbench)
      • Observe their process, fit geWorkbench around it
    • Create a survey/study on the effectiveness of genSpace
  • Project management
    • Create a folksonomy of analyses, tagging them with the task that researchers are actually working on
    • Utilize the logs that we have to create a research log to assist with analyses
    • Allow PI's to track research status
  • Workflow management
    • Allow creating, saving, sharing of workflows
      • Integration with the scripting engine
  • Social Features
    • Add chat, screen sharing, and workflow sharing
    • Add groups
      • "Real" groups - People from lab X
      • "Virtual" groups - People who use tool Y
  • 360° feedback on geWorkbench and genSpace
    • Get feedback from users from within the app
      • Add a context-sensitive feedback loop
      • Provide an optional "Tips" system to push news to users
  • Port genSpace to a web interface
  • Broaden the genSpace website
    • Simple enhancements
      • Search
    • Social networking integration
      • Facebook, twitter, etc linking
  • From the core group:
    • Capturing end/abort of long-duration analyses
    • Improving parameter logging
    • Capturing analyses run on the grid (BLAST, etc)

Account Management Harmonization

We want both geWorkbench and genSpace to use the same user accounts database. The new database should be primed with the existing accounts from genSpace and geWorkbench-desktop if meaningful, i.e., if non-Columbia accounts exist; otherwise we may as well start with a clean slate.

geWorkbench Desktop

  • First time a user downloads and starts the app, they are asked to login (if they happen to already have an account created through geWorkbench-web or genSpace) or register for a new account. We provide a link to a page that explains why we need their info (so that they can use the web version; so that they can use the genSpace component, etc).
  • After the user logs on the app for the first time, we ask:
    • if they wish to store their credentials on disk (encrypted) so that they don't have to provide them each time. If they say "yes", the app remembers them next time the app starts and does not prompt them again. If they say no, they are prompted for passwd next time they start the app (at which point they will again be given the option to change their "save credentials on disk" choice). Users can also change their credential saving preferences from "Account" (or "Preferences"?).
    • to setup their genSpace preferences.
  • geWorkbench updates should retain account info data, so that user should not have to recreate an account/reset their account logon preferences every time the download a new geWorkbench version.
  • Users should be able to log on using OpenId accounts (google, etc).
  • The "Tools->My Account" menu should be changed to the same functionality as the one in the web version, i.e., allow users to change their information (name, contact info, uid/pass).
  • The genSpace component should start in the visualization area, like all the other geWorkbench components (instead of as a popup window). It should be enabled via the "Component Manager".
  • The genSpace component does not have a separate "Login" interface. Instead, when the app starts, the user logs on to both geWorkbench and genSpace.
  • GenSpace usability improvements:
    • Use visible progress bar for operations that fetch data from server. Right now there is a progress bar at the bottom of the genSpace window but it is barely discernible.
    • The first tab titled "genSpace Login" should go or be replaced by a "Preferences" tab that will allow users to setup the logging preferences (should become the last tab). Also, the "General Profile" subtab in there should go as well.
  • The production version of genSpace should be located on the same machine as the server components of geWorkbench.

geWorkbench Web

When logging on

GenSpace component

  • It should open up in the regular visualization area, like all other components. DONE.
  • The "Login" pane should be removed (when users logs on to geWorkbench, they also log on to genSpace) and replaced instead with a "Preferences" tab with functionality similar to that used in the desktop version. DONE.
  • In keeping with treating genSpace like a regular component, it should be selected not from a separate menu item, but rather from the available tools listed when selecting a node in the Projects Area (what others think about this?).
    • Since it is not associated with any particular data set I don't think this is appropriate. genSpace is a system-level component.
  • The Activity Feed in genSpace should be available all the time somehow (if we are serious about it) . One idea would be to add an "Activity" menu item at the top level and also have some type of a warning showing when an interesting event happens (a message is received; a friend logs on).
  • Aspects of the user interface should be redesigned. E.g., under "Workflow Visualization" do: "select action = most common workflow starting with" and "select tool = Aracne", then click "search". This returns one workflow titled "aracne". Based on how "aracne" is shown, one would never guess that it is clickable. Yet it is:clicking on it brings a separate popup titled "workflow actions" (this should not be a popup but instead open in an area within the pane). Clicking on a link or button in the popup results in either trying to open an external genSpace page in the same browser window that geWorkbench is running (this should instead be done in a separate tab) or bring up yet another mini popup. Clearly this is an unwieldy interface that needs to be redesigned in a more disciplined manner.
  • There is no notification that e.g. a friend or network join request has been received. You have to actually go to the Communicator to check this.
  • When you make a friend request, the web version shows the person as a friend even if he/she has not accepted your invitation. The actual status should be displayed.
  • The time window in which successive events are considered to be part of a workflow seems very short. We need to understand how this works and what the time window is.
  • It might be useful to add a method to create a new workflow from events in the Research Notebook. This would remove the time constraint on workflow generation.
  • Clarify that it is data about workflows, not the actual experimental data, that is being shared in the Home tab "Select data visibility options".
  • The genSpace DB should record if an analysis is done in geWorkbench-web or geWorkbench-desktop. But results from both can be co-mingled I think. Mantis issue #3890.
  • The genSpace DB includes numerous redundant analysis names. Names used must be reduced to one per analysis, shared by both desktop and web. Mantis #3889.
  • In Workflow statistics, the "?" icon is not appropriate to indicate expanding a collapsed list. Mantis #3888.

Technical Documents

Retrieved from "http://wiki.c2b2.columbia.edu/informatics/index.php/GenSpace"
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