NeuroCausal - HackMD

--- # NeuroCausal ## Welcome 🙌🏽 ## [Code of Conduct](https://ohbm.github.io/hackathon2020/coc/) reminder * Be respectful, honest, inclusive, accommodating, appreciative, and open to learning from everyone else. * Do not attack, demean, disrupt, harass, or threaten others or encourage such behavior. * Be patient, allow others to speak, and use the zoom reactions & chat if you would like to voice something. --------- ## Neurocausal Resources: - [Gannt Chart](https://docs.google.com/spreadsheets/d/1-eofKKLSfeaD9Kx5pTI1kXNUISzljCvlctDnrMoNBEs/edit#gid=0) - [Website](https://neurocausal.github.io/) - [Github](https://github.com/neurocausal/neurocausal) - [BH Project Pitch Slides](https://docs.google.com/presentation/d/1jUMNjSsjG-25JGaYiKqC1siwH7Ofxht6Td3LML9Nnvw/edit#slide=id.g1334faab463_0_141) - [OLS Graduation Slides](https://docs.google.com/presentation/d/1osNaVnllLPCdtAju4Klc4i0CX2Y8XEHxatyepGxdbH4/edit#slide=id.p) - [Zotero Library](https://www.zotero.org/groups/4704047/neurocausal/library) - [Twitter](twitter.com/neurocausal) - [OSF](https://osf.io/ua7tv/) - [Mattermost](https://mattermost.brainhack.org/brainhack/channels/neurocausal) - [Discord](https://discord.gg/Dbbe6MKjpD) - [BH proceeding](https://docs.google.com/document/d/1GSBEclrMGfF9f5VYy6xPvvpNNTQENi2F3_6b5lUw-6c/edit) - **Project leads' usernames, emails, timezone**: -- Valentina - valentinaborghesani@gmail.com - CET -- Pedro - Pedro.PinheiroChagas@ucsf.edu - PT -- Sladjana - slukic@adelphi.edu -ET -- Isil --------- # Meetings: We meet every **Mondays at 5pm CET** at https://unige.zoom.us/my/nocelab ## Structure - Rollcall - who's attending? - Agree on note taking & schedule (go over pre-compiled agenda if possible) - Wrap Up ### Rollcall - your name - (if new to the group) your pronouns, job & location - what's on your mind/agenda today? ### Note taking & schedule Ideally we: - start by a recap of the status of the project - decide what to tackle (in advance) and work on it (might be independednt silent coding/writing) - take turns on who is taking notes ### End of Day Wrap up & Feedback Meeting - what worked & what not - what should be on the next meeting agenda -------- # Monday August 1st ### Attendance: - Vale (taking notes), Isil, Ruoqi ### Agenda: - status submission BH proceedings -- Isil made PR, waiting on verdict - status contact with [CogAtlas_2.0](https://docs.google.com/spreadsheets/d/1_f6M5ompblVKOxYbRQLmEi4PMHtFO40J/edit#gid=204561229) -- Vale asked for meeting to Seb - status code for filterning cleaning papers & extracting neural space information -- Isil to produce 2 more spreadsheet with the current code -- group to check false positive/negative next meeting # Monday August 8th ### Attendance: - Vale (taking notes), Sladja, Seb, Pedro, Ruoqi ### Agenda: - checking spreadsheet - working on paper downloading - using "clinical + brain" - look at the percentage of the papers downloded that are labelled as clinical - keep working on [CogAtlas_2.0](https://docs.google.com/spreadsheets/d/1_f6M5ompblVKOxYbRQLmEi4PMHtFO40J/edit#gid=204561229) - Vale to write to Russ Poldrack (cc-ing Seb) - Seb to provide list of terms missing from CogAtlas as they encounter them # Monday August 16th ### Attendance: - Vale (taking notes), Isil, Sladja, Ruoqi, Ana Luisa ### Agenda: - any update on BH proceeding? - BH global will be 28 Nov - 11 Dec - which locations are we interested in? - Vale attending Donostia 23rd-to-25th Nov - there might an overlap for Isil with MAIN early December - update on the converation with NeuroBagel/CogAtlas - meeting with Seb: August 22nd, 17 CET - Isil - meeting with Russ: Sept 6th, 18 CET - Isil - revisit results of spreadsheet QC and adjust filtering code - Sladja: what about having key words that HAVE TO be there (e.g. brain)? - Vale: - remove the neural/tecnical terms from the first filtering - remove the hard threshold at "at least 30 clinical words"(currently second column) - only consider papers with more than 400 words - put density threshold higher (from 0.1 to 0.3, currently last column) - update on the papers download process - currently downloading using keywords "clinical + brain" - adding "human"? adding "participants" "subject" "control group"? - apply for Brainhack cloud for heavy processingPeripheral nervous system # Monday August 22nd ### Attendance: - Vale (taking notes), Isil ### Agenda: - updated code pushed to github: seems to be working great - downloading papers: waiting for the BH cloud - are we changing time/date? waiting for email response # Monday August 29th ### Attendance: - Vale (taking notes), Sladja, Pedro ### Agenda: - send a reminder to Russ (if no response before) & create an agenda [here](https://docs.google.com/document/d/1ILc98SA8XQ3NOz9Q-Hs4ZXjYDQfp5YKJr33qoXWgR6g/edit) - check latest iteration of the filterning - Pedro suggesting to add exclusion criteria: - studies with animal models: "mouse", "mice", "rat", "trout", "fish", "Peripheral nervous system", "rodents" (in the title or threshold for frequency in the text) - title ("meta analysis", "review", "promises", promises and perils") papers that not contain raw data. - For the next filter consider counting the words "brain, cortex, subcortical" in the text and their proportion relative to the other terms. If the proportion is too low, like 1/100 we exclude the paper, because it will not contain any brain information. - Sladja suggesting to add exclusion criteria: healthy volunteers (in the title: 23300618); gene/cell data (22844511,20224795); rats (23098894, 16274856,19682547) or animal models. # Monday Sept 5th ### Attendance: - Vale (taking notes), Sladja, Isil, Pedro, Ruoqi ### Agenda: - updates on brainhack cloud: - there is no limit per se, but cost increases as data is kept there - Isil will add other members of the team (done) & create a small instructors - updates on papers downloading: - 85 gigabite of new data - at the final stage of the Neurosynth preprocessing, we hit 8.3 terabite - to-do: draft an email/issue and ask directly to Jerome for help (Isil) - implement changes suggested above WHILE moving on with the rest of the code - to-do: ~~generate oter 5/6 spreasheet of the neural-info-filtering (Isil)~~ - tomorrow we meet Russ & Ross! # Monday Sept 12th ### Attendance: - Vale (taking notes), Isil ### Agenda: - to-do (from previous agenda): - draft an email/issue and ask directly to Jerome for help (Isil) - not done yet because the error might be on us = will be asking for suggestion on handling the data - check out filterning (focusing on neural data extraction) - https://osf.io/mexa6 - missing the basic papers info? = it's [here](https://osf.io/ca8kv) # Wed Sept 21th ### Attendance: - Vale (taking notes), Sladja ### Agenda: - settle on a new day/time based on [this]( https://www.when2meet.com/?16908384-8M9oA): Thursday 8pm - keep working on [grants proposals](https://docs.google.com/document/d/1KnkoGGG7sle4ga_o_TqVtEGrbiEaYC0e29kVC2ArIoQ/edit#heading=h.fo6mutf4a4u80) (off-line) - VB: I have a feeling we should try the R01 for neurocausal (develop informatics tools for analyzing, visualizing, and integrating data) and the R24 for cogatlas 2.0 (develop web-accessible data archives to capture, store, and curate data). # Thursday Sept 29th ### Attendance: - Vale (taking notes), Sladja, Pedro, Isil ### Agenda: - make sure we have compiled a list of Atlases + their region names - [atlasreader](https://github.com/miykael/atlasreader/tree/master/atlasreader/data/atlases) might of help - IB will bring together the csv files with the extended version of the labels - DONE = Isil can you link it here? sorry I lost it - IB will implement the code fromt the 3rd stage of the NQDC for brain label/coordinate extraction - Working on it - keep working on [grants proposals](https://docs.google.com/document/d/1KnkoGGG7sle4ga_o_TqVtEGrbiEaYC0e29kVC2ArIoQ/edit#heading=h.fo6mutf4a4u80) (off-line) - VB to write to Russ on Monday with the current state of affairs - which brainhack(s) are we attending? - VB: Donostia (November 23-25) and Geneva (December 1-3) # Thursday Oct 6th ### Attendance: - Vale, Sladja, Isil, Pedro ### Agenda: - keep working on [grants proposals](https://docs.google.com/document/d/1KnkoGGG7sle4ga_o_TqVtEGrbiEaYC0e29kVC2ArIoQ/edit#heading=h.fo6mutf4a4u80) (off-line) - within 1 week let's have the 2 pages ready - in which brainhack(s) are we presenting the project? - VB: Geneva (December 1-3) - PC: Bay Area (dates TBD) = if there are open issues # Thursday Oct 13th ### Attendance: - Vale, Sladja, Pedro ### Agenda: - keep working on [grants proposals](https://docs.google.com/document/d/1KnkoGGG7sle4ga_o_TqVtEGrbiEaYC0e29kVC2ArIoQ/edit#heading=h.fo6mutf4a4u80) - plans for BH (at least) [Geneva](https://brainhack.ch/#portfolio) and [Donostia](https://brainhack-donostia.github.io/schedule/) - (1) make progress in adapting the code base of Neuroquery (https://neuroquery.org/) to our question == NEED TO OPEN SPECIFIC ISSUES - (2) improve the data source (and possibly structure) of CogAtlas (https://www.cognitiveatlas.org/) == at least [one issue](https://github.com/neurocausal/neurocausal_meta/issues/5) ready - (3) make steps forward on the data sharing side == NEED TO OPEN SPECIFIC ISSUES # Thursday Oct 20th ### Attendance: - Vale, Isil, Sladja, Pedro ### Agenda: - updates on [grants proposals](https://docs.google.com/document/d/1KnkoGGG7sle4ga_o_TqVtEGrbiEaYC0e29kVC2ArIoQ/edit#heading=h.fo6mutf4a4u80) - Tuesday deadline to send it to Russ and Ming Zhan - plans for BHs? - Donostia Nov 23rd - 25th, Geneva Dec 1st - 3rd, SanFransisco Brainhack, first week of - for sharing part, open issue on (1) servers/datalad/etc... + (2) template of data organization - disseminations events - Vale @ Lausanne, Nov 16th - Pedro @ UCSF ? - adapt the cleaning code after checking [current results on OSF](https://osf.io/hjsm2/) - at least one person needs to download it all to check the info below, - others can split and download just bits to check filterning - note down - how many papers downloaded (with which criteria) - Criteria: Clinical + Brain - The number of papers downloaded is 717,601 (85 GB) - ~ 460,000 with text body (the rest of the eliminated papers have only abstract or empty body) - how many pass the first filter (is it clinical?) [This sheets share the numbers of papers passes clinical and then techical filters](https://docs.google.com/spreadsheets/d/1il9I5HVLjwFA7LkF7CziGKgjXCO9IVcEo-OSNtVm_1k/edit?usp=sharing) - how many have MNI coordinates - Working on it! (since the papers idenfied by nqdc as the _papers with the MNI coordinates_ includes unnecessary papers that we are not interested in.) - extract those MNI coordinates [Here](https://osf.io/zdyvs) the document for the data. Considering we are still missing 3 sheet (40 K papers) the reporting in the rest of the papers are as; - MNI reported in 17502 papers - Talariach reported in 2987 papers - check which atlas most used - Harvard-Oxford: 103 - AAL: 4576 - Desikan: 62 - Destrieux: 0 # Thursday Nov 3rd ### Attendance: - Vale, Isil, ### Agenda: - updates on [grants proposals](https://docs.google.com/document/d/1KnkoGGG7sle4ga_o_TqVtEGrbiEaYC0e29kVC2ArIoQ/edit#heading=h.fo6mutf4a4u80): sent to Ming Zhan, no reply - Fixed meeting to prepare for BHs - **to-do Isil**: run the pipeline of NeuroQuery as-is on the papers with MNI coordinates - **to-do Vale**: write to Seb for the bids-ification of the clinical datasets and other sharing-related issues - BH issues opened/to-be-open - sharing - [template and example](https://github.com/neurocausal/neurocausal_share/issues/2) - [servers and datalad](https://github.com/neurocausal/neurocausal_share/issues/1) - meta - [working on cogatlas2.0](https://github.com/neurocausal/neurocausal_meta/issues/5) - close outdated issues and open new ones, e.g. improving the query + dowloading and improving the clinical filtering code - plans for BHs? - Donostia Nov 23rd - 25th, - Geneva Dec 1st - 3rd, - San Fransisco Dec ????? - disseminations events - Vale @ Lausanne, ?? - Pedro @ UCSF ?? # Friday Nov 11th ### Attendance: - Vale, Isil, Seb ### Agenda: - Neurobagel (annotation tool) running in test phase at MNI, then Douglas - check out: https://github.com/datatagsuite - Issues that Vale will handle at the: - [preparing indexing tools](https://github.com/neurocausal/neurocausal_share/issues/1) (google form + spreadsheet populating and behing published) - [preparing template](https://github.com/neurocausal/neurocausal_share/issues/2) - [keeping on writing info on CogAtlas](https://github.com/neurocausal/neurocausal_meta/issues/5) # Monday Nov 14th ### Attendance: - Vale, Isil, Sladja ### Agenda: - TO-DO before BHs: - finding papers among already filtered with MNI coordinates running rest of the pipeline with them - Update the readme with instructions - ~~prep [slides for project pitches](https://docs.google.com/presentation/d/1h2rVJxT6YG-n-NwmWwPxV4wIwMz4gtCydX625WyYAKg/edit?usp=sharing)~~ - Discuss with Steffen regarding the best use of VM by random users during Brainhack events - move the data to object storage so it can be accessible by many new VM instances - Issues for BHs: - [downloading](https://github.com/neurocausal/neurocausal_meta/issues/20): constructing the query using NIH tool + downloading a new set of data with restricted query *** - [filtering](https://github.com/neurocausal/neurocausal_meta/issues/11): improve the filtering code to restrict to human clinical usable data - [adapting nq code](https://github.com/neurocausal/neurocausal_meta/issues/12) to atlas (rather than coordinates), choose atlas, convert all coordinates (and other atlases) to that one **** - [preparing indexing tools](https://github.com/neurocausal/neurocausal_share/issues/1) (google form + spreadsheet populating and behing published) - [preparing template](https://github.com/neurocausal/neurocausal_share/issues/2) - [keeping on writing info on CogAtlas](https://github.com/neurocausal/neurocausal_meta/issues/5) *** require sharing user with Isil so they can have access to the cloud # Monday Dec 19th ### Attendance: - Vale, Pedro, Sladja, Isil ### Agenda: - Update on BH results - BH Bay Area Feb = focus on atlas & neural space - Early January: - send email to everyone with general updates - reach out to Betrand - Spring: grant writing! # Tuesday Jan 18th ### Attendance: - Vale, Bruno, Isil, Ana Luisa ### Agenda: - Will BH BayArea take place? - February 9th and 10th - Margo from Pedro's lab will join to the next meeting - Keep the discussions under the issues for easeness of following up. - Shall we reach out to Betrand/Jerome? - ~~Vale to-do: write to them and propose a meeting to update them~~ - Grant writing: - Vale to-do: - write to Ming Zang to clarify whether to merge or not Neurocausal and CogAtlas - check feasibility of SPARK: https://www.snf.ch/en/8EWqXT6CZ7wuAJUq/funding/programmes/spark # Tuesday Jan 24th ### Attendance: - Vale, Isil, Bruno, Sladja, Margo ### Agenda: - Email to Betrand/Jerome sent, waiting on reply - Started working on code for neural mapping ([matlab code](https://github.com/neurocausal/neurocausal_meta/tree/main/atlas_conversion_matlab_codes)) # Tuesday Jan 31st ### Attendance: - Vale, Isil, Sladja, Ana Luisa, Margo ### Agenda: - general updates + independent working - [notes](https://docs.google.com/document/d/1beQ6S9hO9X8HeAVpIh1Ga53jYHggdwmL0GFCvWMAw98/edit#bookmark=id.4oh43961ujf2) from the meeting with neuroquery people # Tuesday Feb 7th ### Attendance: - Vale, Bruno ### Agenda: - working on grants - resources shared on mattermost (should keep updating our [Zotero Library](https://www.zotero.org/groups/4704047/neurocausal/library)) - https://scicrunch.org/scicrunch/interlex/view/ilx_0109835#children - https://www.cell.com/trends/cognitive-sciences/fulltext/S1364-6613%2810%2900201-9 # Tuesday Feb 14th ### Attendance: - Vale, Isil, Pedro ### Agenda: - general check-in - From Pedro on BH Bay Area: - mostly newcomers, so the time was spent helping people setting up their github/python etc.. - lots of inputs on the sharing side, especially on how to (or not to) encourage sharing in clinical setting; should be reaching outside the classical, uni-related, clinical settings (e.g., private clinics), especially outside the US; need to consider which are the incentives and to establish strict ethic protocols; might be ideal to offer the storage option too (partnership with OpenNeuro?) # Tuesday Feb 21st ### Attendance: - Bruno, Lucia ### Agenda: - No topics # Tuesday Feb 28st ### Attendance: - Bruno, Isil ### Agenda: - Went over the mapping [schematic](https://docs.google.com/presentation/d/1gJQlHV5_uRIEwcFcxpkA0ol2jzfoE1xscvEO-rx6pds/edit#slide=id.g20c3c611a68_0_30) - String weighting to find the best matching atlas from paper reports - Check if they use freesurfer then highly likely they might be using default Desikan-Killiany or Destrueux - Neuroquery has a animal-exclusion list - ~3000 out of 13000 papers reports Talariach (but some of them might be animal studies) # March to August : break for maternity & summer # Friday Sep 1st ### Attendance: - Vale, Pedro ### Agenda: - Where are we now? - Where are we going next? - check new deadline for the BrainInitiative grant NIH - get updates on the code # Friday Sep 8th ### Attendance: - Vale, Sladja ### Agenda: - Where are we going next? - [NIH grant](https://grants.nih.gov/grants/guide/rfa-files/RFA-MH-23-270.html): is this the only one? # Friday Sep 15th ### Attendance: - Vale, Isil ### Agenda: - check in - should try leveraging LLMs now - need to keep in touch with Jerome (now working with Gael) - change the date/time? # Monday Sep 18th ### Attendance: - Vale, Isil, Sladja ### Agenda: - downloading papers (see issue [here](https://github.com/neurocausal/neurocausal_meta/issues/20)) = **do it and put on [OSF](https://osf.io/ua7tv/)** - filtering for clinical papers (see issue [here](https://github.com/neurocausal/neurocausal_meta/issues/11)) = **check after new downloading to ensure we have the best inclusion/exclusion criteria** - neural spaces to be used: [converged on using MNI coordinates](https://github.com/neurocausal/neurocausal_meta/issues/12) = **make sure we have all references to convert the various atlases** - pause the CogAtlas 2.0 [issue](https://github.com/neurocausal/neurocausal_meta/issues/5) - stick with [Neuroquery vocabulary ](https://github.com/neurocausal/neurocausal_meta/issues/3)for now then revise based on the results # Monday Sep 25th ### Attendance: - Vale, Isil, Pedro, Margo ### Agenda: - downloading in process (should finish today) on the brainhack cloud - before the filterning we need the preprocessing step - we'll try runnig the neuroquery code on just those with MNI coordinates (guess: they will be around 200) - Convertion: - from the clinical filterning we know which atlas is used - take the atlas, take the names of all its regions - check which of these appear in the journal # Monday Oct 9th ### Attendance: - Vale, Ana Luisa, Isil, Pedro ### Agenda: - Improvements ahead - Suggestion on improving the clinical filtering: focusing on results/methods (discarding intro/discussion) - Plural forms needs to be added to the technical filtering - Next step - For the papers with the MNI continue with the pubget - investigate how to prompt to chatgpt with the abstract and rules for sanity check - Run the pubget step3 with `--articles_with_coords_only` parameter and run clinical and filter. # Monday Oct 16th ### Attendance: - Vale, Ana Luisa, Pedro ### Agenda: - Isil working on trying the original code on the papers with MNI - Pedro prep the [code for the atlas-to-MNI conversion ](https://github.com/neurocausal/neurocausal_meta/issues/12) - pimp up the website - Predo will prepare demo based on "semantic memory" and svPPA patients = Vale e Sladja to help # Monday Oct 23rd ### Attendance: - Vale, Sladja, Pedro ### Agenda: - [Papers for demo](https://docs.google.com/document/d/1TSty2ih_Y16-_LrMBa8_-krbzEDzQLcqpGBfN845E9k/edit) # Monday Oct 30th ### Attendance: - Vale, Sladja, Pedro ### Agenda: - [figure for website/presentation](https://docs.google.com/presentation/d/1WZ-Uw6hS27xmFmnCSKGg_Rqutb0v8-475GvYIIHFxe8/edit#slide=id.p) # Monday Nov 13th ### Attendance: - Vale, Pedro, Isil ### Agenda: - code running beautifully - things that can be perfected - paper selection (there are still a few not-clinical) - [vocabulary](https://docs.google.com/spreadsheets/d/1i7JerQ7nJIJfzFIlyZs7C6bZX3FIJY5uf9ipS5cL4Gw/edit#gid=67920567) - things to add - papers with no MNI after [conversion from atlas to coordinates](https://github.com/neurocausal/neurocausal_meta/issues/12) - **data issue (now 472 GB)** - need storage, need to (re)run things, need to be nicely linked with website - Isil to ask about Oracle option - [ComputeCanada](https://alliancecan.ca/en/services/advanced-research-computing/account-management/apply-account)? - just storage options - https://www.nature.com/sdata/policies/repositories#general - https://help.osf.io/article/395-storage-add-ons - Isil will backup the data at the local disc - Sharing the brainhack cloud access # Tue Nov 21st ### Attendance: - Isil, Ruqoi, Pedro, Ana - ### Agenda: - should apply for - https://edu.google.com/programs/credits/research/?modal_active=none - https://pages.awscloud.com/aws-cloud-credit-for-research.html - https://www.microsoft.com/en-us/azure-academic-research/ - Conversion - Papers with coordinates that are not MNI (An example [implementation from Ana's lab](https://github.com/DiedrichsenLab/Functional_Fusion)) - Paper no coodrdinates (text analysis) - Integration of all data to the pipeline - Evaluation test needs to be implemented - Prediction accuracy metric - Isil will write a small guidelie with links to the all resourcs and awaiting steps to iterate on that - Meeting with Ana next Monday at 5 pm Canada time # Mon Dec 11th ### Attendance: - Vale, Pedro, ### Agenda: - [Amazon storage](https://aws.amazon.com/products/?aws-products-all.sort-by=item.additionalFields.productNameLowercase&aws-products-all.sort-order=asc&awsf.re%3AInvent=*all&awsf.Free%20Tier%20Type=*all&awsf.tech-category=*all) - use box folder to backup the data # Tue Feb 20th ### Attendance: - Vale, Ana, Pedro, Isil ### Agenda: - we're waiting on Amazon credit grant verdict - we got the Google one (CHF 4,315.51) - need to check out - how to create the project - how to share the project - how to assign the credits - set up a meeting with the google engineers - [Vale to set up a clear sharable gantt chart](https://docs.google.com/spreadsheets/d/1-eofKKLSfeaD9Kx5pTI1kXNUISzljCvlctDnrMoNBEs/edit?usp=sharing) - Try install/run on other local computers and write down the tutorial on github - Try [RAG](https://research.ibm.com/blog/retrieval-augmented-generation-RAG) to get the needed data from the old/not-MNI papers? - Vale to talk to Fabian - Next meeting --> run the model at everyone's local # Tue Feb 27th ### Attendance: - Vale, Isil, Pedro, Ana Luisa ### Agenda: - Isil - looked for options to periodically update the paper downloaded - Vale - wrote to try and set up a meeting with the Google Cloud people = we could book with Ross Thompson one of the next [Tue](https://calendar.google.com/calendar/u/0/appointments/schedules/AcZssZ3ZtY9qN1gSafyNJVse6FArWGzBIfetuHyQ-cVENqnvbDJ4r_glca7naKQaZAUTegMNghAh0QAl) - prepared the [recap of next/current steps](https://docs.google.com/spreadsheets/d/1-eofKKLSfeaD9Kx5pTI1kXNUISzljCvlctDnrMoNBEs/edit?usp=sharing) - shared the [storage](https://cloud.google.com/storage/docs) and [virtual machines](https://cloud.google.com/products/compute?hl=en_US&_gl=1*b2qx5p*_ga*MTgwODkzODc0Ny4xNzA3MTU5ODYw*_ga_WH2QY8WWF5*MTcwOTA0OTAxOS4zLjEuMTcwOTA0OTM3Mi4wLjAuMA..&_ga=2.184313638.-1808938747.1707159860) tutorials # Notes while working asynchronsly ### Agenda: - Isil got access to the google project - updates? - CogAtlas 2.0 - Dr Katie Marie Lavigne, <katie.lavigne@mcgill.ca>, is working on very similar goal (transdiagnostic but coming from psychiatry) and we should keep her in the loop - Similar shared interest with Strasser-Kirchweger Barbara <barbara.strasser-kirchweger@plus.ac.at>, a phd student working on the Austrian version of NeuroCloud / OpenNeuro - best strategy is for Vale to reach out again to Russ P. - do we agree? - Also interested in our work (in general) are [Alexis](https://neuroling.github.io/People.html) and [Narly](http://brainandlanguagelab.org/people/narly-golestani/) (who would like to put us in touch with [Cathy Price](https://profiles.ucl.ac.uk/2488-cathy-price) given her [PLORAS](https://www.ucl.ac.uk/ploras/ploras-predicting-language-outcome-and-recovery-after-stroke) work) - they both stressed how useful the tool will be and how much we need to push for dedicated fundings # Tue April 16th ### Attendance: - Isil, Vale, Sladja ### Agenda: - Data sharing-side of the platform: - adding suggestions and reccomendations for IRB writing etc... - We need to keep track of [Gsoc project by neurobagel on LLM-annotation](https://neurostars.org/t/gsoc-2024-project-idea-19-1-an-llm-assisted-service-for-annotating-research-data-with-machine-understandable-semantic-data-dictionaries-175-350-h/28279/8) # Tue April 23rd ### Attendance: - Vale, ### Agenda: - the description of the LLMs desired steps is [here](https://docs.google.com/document/d/1hrmdOVxWAgFQm2HlaSjKny51b_Q1LY9n2Hc5nRQH3e8/edit) - The cloud usage cost forecast is [here](https://docs.google.com/document/d/19UDBF4p_WpV2MahWiMRNyeDQskRg08nZtmC_lWx722w/edit?usp=sharing)