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ETC Interface

ETC Interface Mockup: File:UAB web template3.pdf

  • ETC Overview

01ETC Overview.png

  • Sitemap


  • Task Manager


  • Header/Footer


  • File Manager


  • File Manager replacement suggestion


  • File Manager replacement suggestion 2016

FileFileManagerReplacement2016-1.jpg FileFileManagerReplacement2016-2.jpg

  • Parsing & Matrix Generation, Step Select

07Matrix Select.png

  • Parsing & Matrix Generation, Step Preprocess

08Matrix Preprocess.png

  • Parsing & Matrix Generation, Step Learning

09Matrix Learn.png

  • Parsing & Matrix Generation, Step OTO

10Matrix OTO.png

  • Parsing & Matrix Generation, Step Parse

11Matrix Parse.png

  • Tree Generation, Step Select

12Tree Select.png

  • Tree Generation, Step Generate

13Tree Generate.png

  • Tree Generation, Step Wrapup

14Tree Wrapup.png

  • Matrix Review Sketch



  • Taxon Concept Comparison Sketch


Suggestions Heshan

  • Consult the end-users regarding work process and output formats e.g. trees.
  • Show the status of progress bar on each page, for each task. Address the process which takes more time.
  • Order of characters in matrix
  • User should be able to input the name of the tree when the tree is generated instead of tree1, tree2 etc.
  • Full screen option button for tree.
  • Consult the end-users for requirement of sharing tasks – if the users want to work on the same dataset, share all the processes and the 2 users should be able to work on the same dataset at a given instance.
  • Consult the end-users – How helpful is this tool.
  • At the end give a summary report which includes e.g. number of words, sentences etc.
  • First page – should have a simple look
    • Include overview in manual, there is no need to show that all the time
    • My tasks – show only task name and progress bar, add a button to show the other details.
    • Similarly, add a button to show Shared tasks
    • Only list the task names, do not include details here
  • We should do some research on wait time management. I will check the literature for some better ideas.
  • It is important to solicit more realistic user requirement through interviews and a survey question. We need to identify the sample.

Heshan meeting 2

  • Time Management:
    • Expectation: Tell user in advance about what delays he may expect.
    • Process transparency: Tell user how much time is left as much as possible (progress bar), Tell user what is actually happening (“currently copy file X” etc.) Similar to installation process of a software.
    • Hong’s interviews suggest that users do not want to know what is going on in detail. Hence we do not tell the user what is happening in detail, but provide instead only a message when an error occurs.
    • Email notification upon completion of process
  • File Manager Simplifications: More Windows Explorer like
    • Remove folder categories, instead use color if differentiation necessary
    • Remove File Tab and instead give a progress bar next to a file to show its processing progress
    • Remove Merge column, instead allow drag & drop like move of files
    • Allow rename of folders by click
    • Upload format check should not display check boxes but rather a tick
    • Additional File encoding check necessary
  • Overview page:
    • The task description should be shortened. Give Input/Output information in a mouse hover dialog and the respective Task only.
    • Task text shouldn’t be given the ‘technical’ names we use but rather something the user can grasp quickly. (e.g. Euler)
    • Task text should match the diagram. ETC Pipeline label over the diagram.
    • Navigation Tabs that allow quick access to create a new task: Tabs: Overview, Task1, Task2, Task3, Task4, File Manager.
  • Task pages
    • Input and Output instead of Select/Upload Files and Wrapup Task are more intuitive.
  • Usability Study
    • Drop & Compute Style approach vs. Website Mockup (runnable with sample data)
    • Which do users prefer
    • Why or which parts do they dislike one of the two variants (workflow, wait time, output..)
    • Need about 20-30 users, ideally biologists.
  • Drop & Compute with Dropbox
    • Find out whether it may not be ok to share folders with ~100 users on dropbox.

Other Suggestions

  • Instead of Task Files view use a folder in File Manager to contain all the files of a task
  • move file check (e.g. for brackets) from a task to the upload of files. Any problems with the files should be fixed by the user during the uploading process.

Meeting 10/25/13: Markup, Matrix Generation, Sharing

Markup MatrixGeneration Sharing1.jpg Markup MatrixGeneration Sharing2.jpg

Interactive Key GUI Proposal by Cui

File:Interactive Key GUI Proposal for Shizhou.docx

iPlant Collaborative

iPlant Datastore

  • Introduction
  • Users have an initial allocation of 100 GB.
  • Additional allocation up to 1 TB can be requested by sending a short justification to iPlant Support.

Discovery Environment


Euler Workflow


Euler Mock-up draft 1 by Shizhou Yu

  • Header


  • Input Files Manager


  • Get Started


  • Check Consistency


  • Inconsistency Explanation


  • Get MIR


  • Reduce Ambiguity


  • Display Merged Taxonomies/Datasets


  • Statistics


Comments to Euler Mock-up Draft 1


Euler Mock-up Draft 2: Euler Alignment Explorer (EAX) by Bertram


Euler Mock-up Draft 3: Euler Alignment Explorer (EAX) by Cui

EAX cui.png

Euler Mock-up Draft 4: Euler Alignment Explorer (EAX) by Franz

  The "highlighting" will be neat to develop. Things that a user ought to be able to say about a selected concept, with different colors.
  • Done with this one.
  • This one's urgently pending.
  • Not sure, perhaps return.
  • Unmarked.
  • Suggested for articulation by Euler Wizard.
  • Causes inconsistency (a global phenomenon with local solutions).
  • Causes ambiguity.
  • Has the following articulations currently.

EAX Franz.png

Euler Mock-up Draft 5: Articulation generation and evidence


GNITE demo and conclusion

We like the idea of being able to extract the classification from the parse and being able to visualize it as a tree similar to the GNITE presentation. We also like the idea of being able to compare two contrasting classification concepts side by side. We could then go further and have some actions be possible through clicking on a given taxon in the tree. We could summarize for each taxon what characters are making them unique based on entropy calculations from the matrix, We could also allow a comparison of the characters that are making taxa unique between claasifications concepts potentially. This is getting closer to the automated articulation idea. We may be able to suggest which taxa among concepts are the most similar. We could also provide the functionality of merging trees based on these similarity measures. That would be very interesting! We could color (decorate) the tree to show where there is good alignment and where there are problems which would help users identify where they need to focus their attention. I think a visualization like this would be very valuable and probably fulfill our requirements. If we can get this far then it would be easy for us to show the path toward automated articulations.

other concept related works

Concept Mapping Cleistesiopsis

Taxonomic Tree Tools


SEEK tools: ConceptMapper

[1] File:Franz-ABQ-Jan2006final.pptx

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