Sharing Data - User Meeting: 26/11/2010

[saloynton]

Attending: Charlotte, Pedro, Scott Loynton, Aleksandra Tarkowska

Aim: The aim of the meeting was to get some feedback from the scientists and their experience and use of sharing data.

Overview: Charlotte and Pedro are collaborating within and sharing data within the one project. They are currently in the early phases of the work both Charlotte and Pedro are importing data however the longer term goals of the work shall mean Charlotte takes over more of the role of data acquisition and Pedro focuses on the data analysis.

(Notes moved to comment)

[jburel]

Moved from sprint 2010-12-09 (21)

[jburel]

Moved from sprint 2010-12-23 (22)

[jburel]

Scott: any particular reason to have that story attached to a sprint?
This should not be the case. Note that I cannot open the story in firefox.

[jmoore]

Original notes from description:

Requirements:

• They want to be able to discuss about the data.
• There workflow is shared both have equal
• They wish to make use of both PI’s involved in the project and wish to be able to present summaries of their data to the PI’s.
• Both PI’s will want to see the summarised data and be able to make comments.
• The ability to reference/link back to existing work through the discussions would be valuable. (The share scenario being discussed with a PI can be likened to an online conversation about the selected image data)
• The ability to add more images to the share. This is to accommodate the evolution of share through time.
• The ability to invite more people to the shared space.
• The ability to put email addresses in shared spaces, to notify others.

Notification for shared imports on a Project:

• The email title should be clear enough to alert the user what the email is about otherwise people will not read it.
• A subscription (potentially similar to those used in email lists) should allow the user to choose between a notification of each import and a summarised one per day notification for a shared project.

General Feedback

• The option in the home page to resume the last set of actions where you were working on e.g. comments, tags.
• The ability to view the last set of activities of the users in the shared project. Both users had a personal preference of viewing their own last imported image data. So this may require options to view further options on the users home page.
• The ability for a user to see their own comments.
• The ability to edit comments.
• The ability to have an auto save of the scientists work. (Or if in a secure environment the logging out maybe redundant as the scientists working between the bench and office.)
• The potential for limited calendar functionality based on the organisation of meetings around the shared data.

Other conclusions:

• The scientists in Charlotte’s laboratory people are already very used to working with a very open system. They are all happy to have shared data and because of their overlapping scientific work do look at similar projects because of their own future interest.

Potential immediate fix:

• Provide them the ability to view imported data by other users. Change required on Nightshade.

Background

Charlotte started her research in April 2010 in the Jennifer’s laboratory. The position is her first post-doc. The research work in Jennifer’s laboratory is centred on investigating the role of the signalling processes that control multi-cellular behaviour exhibited by single-celled bacteria.

The laboratory uses the bacterium Bacillus subtilis as a model organism to investigate the molecular mechanisms used by bacteria to form social communities called biofilms, which represents the way in which bacteria grow in the natural environment. Recent technical advances in the ability to analyse the activity of single bacterial cells, rather than the total population has revealed that within a biofilm genetically identical populations of bacteria include a number of subpopulations under specific conditions. Charlotte’s research is interested in understanding why subpopulations of cells have different cell fates. In order to examine cell fate differentiation, real time single cell analysis is essential. To do this Charlotte is collaborating with Pedro who is setting up and optimising single cell time lapse microscopy of B. subtilis microcolonies established from a single cell. The B. subtilis cells used carry fluorescent reporter fusions to various gene promoters allowing transcription of genes essential for biofilm formation to be monitored over time (Charlotte 2010).

This is investigating the variations within cells and the variation of tasks that are performed, her work and questions relate to why cells will do one thing and not another. The collaborative work is using fluorescence microscopy to find transcriptions of different genes. This relies upon imaging cells over time to find out how they behave.

The collaboration is in the early phase of the research work and both Pedro and Charlotte are involved in the data collection. Pedro is helping to train Charlotte in the use of the microscope and generate the required data, though in the mean time Pedro is acquiring some initial data. This shall ultimately tip to where Charlotte is leading with acquiring the data leaving Pedro to focus on the analysis of the image data. But the collaboration will still require Pedro’s role to gather and import data occasionally. The annotation and discussion of the data will be equally shared between them both, this part of the process is significant as it will allow them both to have a scientific discussion on the data. The ability to reference the data and data sets along the way would be valuable in supporting the discussion of the data.

The conversation on the data will be shared with the two different PI’s also involved in the project. But this is with the difference that it would require Pedro and Charlotte to take summaries of the data and a summary of why the particular data has been selected so as to be able to share with them. The scenario presented was the ability to select some movies from the data set and allow for the work to be presented, compared and contrasted with the ability to add comments. The utilisation of the roles of the PI’s by Charlotte and Pedro would also look to draw on the PI’s differences in backgrounds and scientific experience so there would be different scientific discussions that take place.
In this scenario the share would undergo evolution as the data in the project grows and the subsequent discussions grows. Because of this the ability to add images and reference back to existing work already carried out relevant to the discussion is seen as a requirement. An example discussed was how a PI may suggest a way of testing the experiment but previous data already demonstrates the technique has been tested. The concept of a share in this way must be able to able to be flexible and grow as the work grows.

The ability to give a link to shared data with users that are not currently part of the OMERO system through email is still a very much a desired piece of functionality. Pedro highlighted how this would allow users that do not necessarily require an account ability to view the required information.

Charlotte spoke of how her laboratory was already very open and already has shared access to scientific data (on their own storage sever?). The laboratory will openly look at each other’s different data sets. So she had no concerns at all in allowing other scientists in her laboratory access to the data that is collected. There are potentially several scientists in the laboratory that the data would be of some use to in the future. Charlotte mentioned that because of the close relation and similar work that is conducted in her laboratory other scientists can and do benefit in viewing each other’s data.

Both Charlotte and Pedro have limited use of existing collaborative web based tools and so had few comments on their positive experiences. Charlotte has received various links to view her friend’s photos but has not used those tools herself.

There was a long discussion on how best to handle notification messages and updates from the shares and the appropriate ways in alerting the users that are part of the shared group. This was especially relevant to the scenario of work between Charlotte and Pedro, as they would both like to be updated when each other has imported data. In the meeting two possibilities were discussed option 1) A daily summary about the image information imported. This would be similar to email digests e.g. ImageJ list.

The feedback for the front page of the client was that Charlotte would like to be able to work on the data that has been imported by Pedro and vice versa. This is currently possible to on the server but would require confirmation in OMERO team in order to be turned on.

Charlotte was experiencing problems in seeing her own images when logging into the front page of the web client. This raised a discussion on what further information should be presented on the home page when logging into the client Charlotte asked what images should be presented and assumed it would be last imported, where it is actually the last acquired images.

Pedro highlighted that is would be useful to have links to that last set of activities carried out such as last set of tagged images, last comments. This would help the user pick up their work from where they last left off.

Charlotte also mentioned she was having problems in seeing her own comments on images. The current functionality of the web client does not allow the user to see the comments that they make unless a user was to make a comment back. Charlotte would like the ability to make comments and view them about her images without having to have the comment shared. The ability to edit comments in the web client is also a desirable functionality as it can be done in insight.

There was an inconsistency raised in the way the thumbnails are viewed between the web client and insight. (Check with Ola?)

Charlotte was also experiencing problems in how the web client can log her out and as a consequence she can loose work. This is part of how she typically works as she may have incubation periods where she can sit at her desk for 15 minutes but then be required to go back to the bench to continue with her experiment work. She needs the reassurance that when she walks away that her work will be saved. Pedro has had positive experience of using the laboratory ordering system (Pecos) it uses a quick save button to save orders so that the order list is not lost.
The scope for this work and concerns over the security is that they both felt when using the web client at work there computers were secure and would be happy not to have the client not log out. But they both realised that this would be different if they were using the client in a public location.

The final discussion was the potential for a calendar. The main point highlighted in this discussion was that it is fundamentally difficult to capture and be able to accommodate for everyone’s way of working with a calendar. With the additional added complexity of potential interoperability issues between calendars. Pedro was working with a paper-based diary and so had little potential use for an online calendar. Based on this, there was scope for potential for reminders of the meetings/events required for the image data. This scenario discussed was a PI planning a meeting to review the data sets that had been shared. The ability to then have the web client serve as a tool to help arrange and confirm meetings around the shared image data was of interest to Pedro.

[eehill]

assigning to web-team now that Scott has left.

[jburel]

To be handled by trello card
​https://trello.com/c/Fe5Kzjkf/53-share-full-review-scoping