M1-12 Proactive onboarding of services and models

elisabettai commented 2 years ago

Original Wrike title: "Increase User Base & Available Resources"

Proactive onboarding of services and models, with focus on SPARC and ANS neuroscience needs (e.g., by contacting authors of SPARC-relevant modeling publications). Deliverable: Services and models on o²S²PARC. Targeted number per quarter: 1-2 services per quarter and 2-3 models per quarter (assuming models can be onboarded using existing services capabilities, e.g. Jupyterlabs). Deadline: Month 1–12

(NIH comment to SIM-Core: “Bring more autonomic neuroscience models and simulations into oSPARC. It was terrific to see oSPARC being used for high-impact modeling studies this year (somatosensory and brain stimulation), but those studies were not within SPARC’s domain area”; SC feedback to SIM-Core: “Build and feature models generated from actual SPARC data.”) Relates as well to Publication on Portal (#684)

See Y6 SIM – 7. Sustainability: Focus on Sustainability for related milestones.

Wrike M5.2

### Tasks
- [ ] New version sim_gui-app/web (deprecated)
- [ ] New version tvb-app/web (deprecated)
- [ ] EIT/Kirill's use-case: Update EIDORS Service @elisabettai
- [ ] EIT/Kirill's use-case: Additional mesher service? @elisabettai
- [ ] https://github.com/ITISFoundation/osparc-issues/issues/942

### Jelly Beans
- [x] CC lab models: finish service creation and submit for publication on the Portal
- [x] Codeathon 2022: submit 6 studies for publication on the Portal
- [x] Publish BIOS (ask authors before)
- [x] Follow up with OA, they have studies on oSPARC that could be published
- [x] Follow up with ZD: he said their work might be ready for Jan/Feb
- [x] Follow up with Raj (AN): AN was interested in putting models on oSPARC
- [x] Maybe, depending on outcome of above: update ASCENT with their requests

### Pastel de Nata
- [x] Check progress with Omkar, support for service creation (service creates an opencor config) if needed
- [x] Follow up with Zach: he said their work might be ready for Jan/Feb
- [x] Maybe, depending on outcome of above: update ASCENT with their requests
- [x] Other: call on Fri 19 May with Kirill
- [x] Call with Sergey

### Sprint [WaterMelon](https://github.com/ITISFoundation/osparc-simcore/milestone/46)
- [x] New version of jupyter-chaste @elisabettai https://github.com/ITISFoundation/jupyter-chaste/pull/1
- [x] Turn [opencor_Config_osparc_service](https://github.com/OmkarAthavale/opencorConfig_osparc_service) into a Service @elisabettai
- [x] Onboard k-Wave (simulator for acoustic simulations in C++, GPU-optimized) @elisabettai https://github.com/ITISFoundation/k-wave/pull/2
- [x] Cardiovascular Simulink/MATLAB model from RP (SPARC group) @elisabettai https://github.com/ITISFoundation/CardiovascularControl-DBI/pull/1

### Sprint Sundae
- [ ] List above a task for every new service to be upgraded @mrnicegyu11
- [x] New version of kember-viewer (deprecated) CRITICAL @odeimaiz. Kember viewer has been removed, there's no replacement yet
- [ ] Add deprecation mark to all legacy services (based on excel list) @mrnicegyu11
- [x] Make "generic" plotting service: use-case: visualize output of [CardioControl-DBI service](https://github.com/ITISFoundation/CardiovascularControl-DBI). It should be accessible to Guest users as well. @elisabettai https://github.com/ITISFoundation/voila-viewer
- [ ] https://github.com/ITISFoundation/osparc-issues/issues/998
- [ ] Sergey LU: Make 3 services out  of Sergey's Matlab scripts @elisabettai

elisabettai commented 2 years ago

Update on sprint Vaporwave

Done

Created 5 new studies with tutorials from SPARC Fair Codeathon

Ongoing

6th study from SPARC Fair Codeathon, blocked by problem with JupyterLab widget (ipyleaflet), opened an issue in ipyleaflet repository

Open

Publish studies on the Portal: I will attend K-Core office hours on Oct 13

elisabettai commented 1 year ago

Goal for sprint Mithril

Onboard new services

JupyeterLab with tvb-recon and other neuron packages (e.g. FSL), as requested by TN and EN.

Onboard new models (as comp. services)

New (updated) cardiac model from CC lab. We received source code in C++, we need to check what is different from existing models and publish new versions/models as appropriate.

elisabettai commented 1 year ago

The NIH would like to have more (oSPARC) computational studies published in this section of the SPARC portal.

EI and EN met to define priorities, for this sprint will try to:

Goal and outcome for sprint Jelly Beans

Priority 0

[x] CC lab models: finish service creation and submit for publication on the Portal
Priority 1
[x] Codeathon 2022: submit 6 studies for publication on the Portal
[x] Publish BIOS (ask authors before)
Priority 2
[x] Follow up with OA, they have studies on oSPARC that could be published
Priority 3
[ ] Follow up with ZD: he said their work might be ready for Jan/Feb
[x] Follow up with Raj (AN): AN was interested in putting models on oSPARC
[ ] Maybe, depending on outcome of above: update ASCENT with their requests

elisabettai commented 1 year ago

Update for sprint Pastel de Nata

Done

Updated ASCENT services (runner and jupyter) as per their requests and to sync with latest version of their repository
Supported Omkar who's using the cookie-cutter
Followed up with Zach to see if there's something to onboard
Asked to kWave authors about making it a service (MatLab toolbox to simulate acoustic wave fields)
Followed up with Max about publishing cardiovascular model (OK, but start in July)
Submitted all we had to K-Core for publication on the Portal (CC Lab new pipeline, BIOS VNS calibrator, 6 codeathon projects)
Followed up with Raj

To do

Follow up with Sergey for demo of LU decomposition with MS's use-case
Follow up with Kirill

pcrespov commented 1 year ago

Sprint WaterMelon

Follow up with Sergey for demo of LU decomposition with MS's use-case
Follow up with Kirill

demo services

elisabettai commented 1 year ago

Update for sprint Watermelon

Done

Update legacy interactive services: new jupyter-chaste service and open-sourced the code.
New service: k-Wave (simulator for acoustic simulations in C++, GPU-optimized). Awaiting feedback from users
New service: Cardiovascular Simulink/MATLAB model from RP (SPARC group) + template to be published on the SPARC Portal.
Followed up with Sergey and received his Matlab scripts for LU decomposition (added task in list above)
Followed up with Kirill and planned to onboard new version of EIDORS and new mesher(?) (added task in list above)

To do

See tasks list above

elisabettai commented 1 year ago

Update for sprint Sundae

Done

Made a reusable voila viewer service, so we don't have to craft every time a new service for plotting simple graphs and share templates with anonymous users. See code and instructions here.
Made a template on master to assess security of the viewer for anonymous users, see this case.
While we assess the security of the voila-viewer, a custom viewer was made for the Simulink Cardio model we recently onboarded, so that we can share it with anonymous users without concern. The provider of the model approved it for publication on the SPARC Portal.
Updated the jupyter-ascent service with the last small/cosmetic/usability improvements received from NP.
Received approval from NP to publish the three ASCENT templates on the Portal. Metadata for submission to the Portal were prepared and shared with NP. The three templates are already public on oSPARC.

In progress

Test the oSPARC ASCENT implementation with a dataset from the portal. Blocked for the moment for a weird COMSOL error that we're debugging.

Todo:

Run MATLAB code from prof. Makaroff and turn it into comp. services on oSPARC.
Check what we can do already for Kirill in terms of onboarding.

elisabettai commented 1 year ago

Update for sprint Baklava

Done

Cardiovascular System model from MH (NeuHeart): a template is now public on osparc.io (needs login because it's a JupyterLab. It has also been submitted for Publication on the SPARC Portal.

In progress

FMM-LU Services (Matlab) code from prof. Makaroff.
- Code runs locally in Matlab, apart from LU decomposition that requires at 128GB of RAM.
- Done first draft of modularization

Blocked

Test the oSPARC ASCENT implementation with a dataset from the portal. https://github.com/ITISFoundation/osparc-issues/issues/998. Weird COMSOL error and ASCENT devs didn't help much so far.

elisabettai commented 1 year ago

Closing this one and moved the remaining tasks to the new issue for Y7 #1093 The list of what has been onboarded in Y6 is in the wrike ticket linked in the description.

ITISFoundation / osparc-issues