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Isak Sylvin edited this page Nov 26, 2024 · 39 revisions

2024-11-26

Present; MOD; EB; VC; IS Listening in: LL

2024-11-19

Present: MOD; JB; EB; AEL

  • MOD is blocked and needs to have an endpoint to start working with real life data
  • EB will focus on getting a endpoint with the QC date up and running as per https://github.com/genomic-medicine-sweden/meta-vis/issues/6
  • EB and IS have little time for this until end of November
  • AEL and MOD will try to create some wireframe mockups so it's easier to show what we want to have

2024-11-12

Present: MOD; IS; EB

  • EB blocked on progress due to other projects
  • MOD Finished first view, added AXios connection. Should be able to add second view. Will add additional views and look further in AXios config.
  • IS blocked from mock data, but has a general overview
  • IS/EB blocked throughout Nov. Can cause issues with EoY delivery.

2024-10-29

Present: MOD; IS; EB

  • Pågående utv. QC endpoint. Moe blockad f. QC sida.
  • Kommer försöka fortsätta på andra sidor.
  • Pågående arbete göra mock data mer realistiskt.

2024-10-15

Present: MOD; IS; EB

  • Dynamiskt skapa nya GET API calls efter frontend mock (se PR #27)
  • Get för alla "samples"
  • Get för keyad sampleID för QC-page
  • Moes IP greenlit
  • Authentication, Oauth VS brandvägg
  • Notis: det får inte förekomma processlogik i frontend; tsv använder oss av bulk GETs.

2024-10-01

Present: MOD; IS; EB

  • Database is accessible GB:
  • Efterfrågas möte gällande API användning MOD:
  • QC view up already
  • Krona and Metadata in pipeline

2024-09-11

Present: JB; MOD; EB

  • MOD: Basic react app; wireframe in Figma.
  • EB: On standby for now

2024-09-03

Present: IS; MOD; EB

MOD; Repository Meta-vis-ui. React n styling app base up. Still setting up fundamentals. -> Put in monorepo.

AL on short pappaledighet. Means any coord w Taxprofiler team halts. MOD requests one endpoint per view for better SWGR support. Decided to keep view-count down (within reason).

EB to generate relevant endpoints

Meta-vis will have SWGR support. We will investigate using OAuth for Login support. Relatively few users. Possibility for KISS system.

2024-08-20

Present: IS, EB, JB, MD

Latest updates of API https://github.com/genomic-medicine-sweden/meta-vis/tree/dev-dataparsing

MD will setup React stack

EB will standby to update API as needed

IS will look into spec'ing front-end

Stockholm still needs to provide a decision on IP/hosts to whitelist for mongoDB access. @pbiology

2024-06-20

Cancelled due to scheduling issues.

2024-06-04

Participants: Anders L (Sthlm), Erik (Gbg), Lokesh (Lund), Isak (Gbg),

  • Update backend dev, Erik
    • Have created a simple API up and running. Built with FastAPI.
    • Want to create a service for it on the mongoDB hosting server
    • Will make it public facing.
    • Have been working with some dummy data just for testing purposes.
    • Need to set up some credentials for it for authentication.
  • We need to have some way of transforming the taxprofiler output into a format that can be loaded into the backend, and then do the loading.
    • Anders L can talk to Sofia to see if taxprofiler (or meta-val) could be made into creating a aggregated output
  • IP range restrictions for DB access.
    • Perhaps we can use the tunnelblick VPN range in Sthlm. Anders L can check if there is a reasonable range to use.
  • Moe gone for 5 weeks on vacation

2024-05-21

Participants: Anders L (Sthlm), Erik (Gbg), Isak (Gbg), Moe (Sthlm), Jonas (Lund), Frans (Örebro)

  • GMS_16S, Frans
  • Update backend dev, Erik
    • Working on the documentation
    • Getting a better understanding of the taxprofiler output
  • Other:
    • Tracking of control samples and how the connect to samples. Jonas will add a user-story
    • Erik/Isak could try to get a very basic endpoint up so we can start thinking about the front-end
      • Endpoint built using FAST-API
    • There is a VM with public access to use for this project in GBG

2024-05-07

Participants: Anders L (Sthlm), Erik (Gbg), Isak (Gbg), Moe (Sthlm), Lokesh (Lund), Jonas (Lund)

  • Status update from Erik (Backend)

    • Started building a simple API for the DB and parsing of the data from taxprofiler

  • Road forward

    • Erik could get some help in thinking about how to store OTU table info in a mongoDB document
    • Would be good to have a few use cases. We make this a-sync in a wiki in this repo
      • From research perspective
      • From clinic perspective
      • From a epidemiological perspective
      • From use cases, think about a mock-up

  • GMS_16S as part of the project?

    • Anders will invite Frans into these meetings

2024-03-22

Participants: Lokesh (Lund) Jonas (Lund) Mo (Sthlm)

  • Lokesh looked into taxprofiler test run with results and understood that the pipeline actually generates krona plots for all the samples that go through the pipeline.
    • Based on that, we were thinking of ideas how to bring the krona plots to the front end directly.
    • Also, we were thinking of highlighting the pathogens in the front end either directly on the krona plot
    • or maybe even have a highlighted list on a separate widget.
  • Lokesh had a meeting with Lili in relation to meta-val and we were discussing and planning on how we could join forces!
    • As the pipeline is already building on the nf-core backbone, we discussed how and where we can start writing modules for the pipeline
    • We will have a follow up meeting on the 3rd of April to plan more in detail how we can tie-up the taxprofiler results to the meta-val

2024-03-08

Participants: Lokesh (Lund) Jonas (Lund) Mo (Sthlm)

  • Lokesh looks into mapping #18 and the interactive krona plots #8
  • Isak/GBG will still be the ones building the backend/API when they are back
    • Anders will get back to Marcela if there are any options to Isak here, or if we just should just put the backend on hold until he is back
  • Moe can help with wireframing and UI mockups when we have some concrete ideas from Lokesh

2023-11-29

Participants: Isak (GBG)

  • MongoDB dev VM has been mounted through Azure at 51.12.241.19. Standard clients are compatible and changes can quickly be requested.
  • Viruspool from taxprofiler has been received. Trying alternate sharing due to some technical issues
  • Process to integrate more GBG members into development is still ongoing.
  • Process to populate schema with semi-realistic data is still ongoing.
  • Still haven't evaluated meta-val output
  • Suggesting next meeting 13/12 15.00

2023-11-15

Participants:
Anders L (Sthlm), Isak (GBG)

Agenda

  1. nf-core dev alignment
  2. Taxprofiler add-on pipe: meta-val
  3. Dev environment
    • Could perhaps host in future, but not so much for dev work.
    • @pbiology will look into setting up a dev VM in Stockholm
    • Ask Sofia again to send Isak example data
  4. Update from all devs Isak:
  • Talking to IT about setting up a dev env
  • WIll try to start trying populations to DB
  1. Other
  • Next meeting on 29/11 @ 15.00

2023-11-02

Participants:
Anders L (Sthlm), Sofia (Sthlm), Isak (GBG), Jonas (Lund)

Agenda

  1. Sofia shows output of Taxprofiler
  2. Discussions on how to build a DB to collect
    • Raw output from classifiers so krona can be re-built
    • Don't have OTUs as separate documents
    • We can talk with the Taxprofiler dev gang about making a JSON file which pretty much have what we wants
  3. Next steps
    • Continue defining the DB schema via json files. Try to nail some sort of first idea, then we can move to building endpoints
  4. Next meeting
    • Date: 2023-11-15
    • ToDo:
      • A MVP schema completed - Isak
      • Example dataset - Sofia/Anders
      • Dev environment - Anders
      • Sync with Taxprofiler dev team - Sofia

Notes

  • Having clinicians build collections of OTUs which should be flagged. For instance all E. coli should appear as red
    • Should also include sample type
    • Differentiate between risk pathogens and known contaminants

2023-10-30 Dev meeting

Participants:
Anders L (Sthlm), Isak (GBG), Jonas (Lund)

Agenda

  1. Dev resources going forward
  2. Ambition and deadlines
  3. Tech stack
  4. Design principles
  5. Dev meetings - Frequency and dates

Dev resources going forward

  • Stockholm & Gothenburg has 600k each for 2023 & 2024 - 0.3 FTE per year per site.
    • Frontend from Stockholm - Starting Feb 2024
  • Lund will most likely move some resources from sc2reporter to here.

Ambition and deadlines

  • Deadline very dependent on techstack and ambition

Tech stack

  • Lessons learned from sc2reporter
  • Backend in noSQL (mongo)
  • Frontend in webdesign language (React, Vue, etc...)
  • One should not dismiss Flask. More people with know-how

Design principles

  • Lessons learned from sc2reporter
  • Think about backend schema
  • Endpoints for a split front/backend

Dev meetings - Frequency and dates

  • SUGGESTION: Every week @ tuesdays @ 15

Follow-up

  • New meeting with a Taxprofiler dev to show what is available and where
  • Think about how this fits in a mongo schema

2023-10-18 Follow-up wish-list

Participants

Stockholm: Anders L, Lili, Tanja, Samuel
Gothenburg:
Lund: Jonas
Uppsala: Tomas C, Claes
Linköping: Jenny
Örebro: Mårten L
Umeå:

Agenda

  1. Round of feedback from each nodes.
    Lund: Initial list covers more or less what we want. Long-term goals might be hard to do. Export function which facilitates import to hospital LIMS would be great. Any structured data like JSON would be fine.
    Uppsala: Talked to micro group. In general happy. Would be good to export a pdf/html report. Metadata in terms of where sample is from would be good for report.
    Örebro: Initial list seems sufficient. Paula had the feedback that historic data to show if something has been seen before would be quite interesting.
    Linköping: Like the current Krona visualisation. If we could also visualise mapping against pathogens that would be good.

  2. Establish developers group.

    • Örebro not really any resources
    • Uppsala, this isn't quite high enough prio to put resources on.
    • Lund, don't really have the people skilled in these kind of analyses right now. Might be people coming in.
    • Stockholm, will add in front-end devs when they return to work/ are hired (Q1 2024). Bioinformaticians quite interested and will try to join in dependant on time.
    • Linköping, don't really have any resources to devote to it. Not from the regional side.

  3. Establish the work method for the dev-group. Meeting structure etc.

  4. Set up first work-meeting for architecture and design.

    • Anders L will call to a work meeting, will sync with Isak. Jonas wants in!

Project management

  • Coordination by developer-meetings (more often) and stake-holder alignments (less often)
  • Code contribution via code-review
  • Information and feedback from non developers via stake-holder meetings.
  • Dev group would benefit from a leader

Expectation of developers

  1. Active contribution with code
  2. Have resources to spend time on project
  3. Be available for developer-meetings

2023-09-29 Upstart meeting

Participants

Stockholm: Anders Lind, Tanja Normark, Samuel Lampa, Sofia Stamouli, Lili Li
Gothenburg: Isak Sylvin, Aisha
Lund: Jonas Björkman
Uppsala: Claes Ladenvall, Tomas Cumlin

Todays meeting

  1. Describe the project
  2. Establish network of stakeholders
  3. Set up a working model for the project
  4. Feedback on MVP

Introduction

  • Part of the PLP Pandemic capabilities call (RePLP-1)
  • Work package 3 - Metagenomics

Visualisation of metagenomics analysis results:
An interactive visualisation tool will be built utilising the technical frameworks from the SC2Reporter. This tool will help guiding decision making by visualising sample composition and key QC metrics. To further increase the utility, a backend will be established where sample information can be stored for data aggregation and cohort level analyses. This will help understanding trends in the data both over time but also between samples in a given series. Apart from being valuable as a tool for epidemiological trending, such a visualiser will also find use in clinical microbiology for viewing metagenomics data from patients. Besides microbial composition, we aim to add qc metrics, diversity scores, flagging of known pathogens, resistome makeup and trending tools to help compare a given sample to known healthy samples.

Stakeholders

  • Gothenburg and Stockholm initial drivers.
  • Any other party who are either wants to actively contribute to the project and/or are interested in the final product

Project model

  • Gather feedback on features
  • Set up a developers group who meet regularly
  • Roadmap for MVP and future releases
  • Development similar to sc2reporter. Split frontend/backend. Tech-stack examples (not decided upon):
    • Backend in mongo
    • Frontend in React

MVP features - Initial thoughts

  • Output from nf-core/Taxprofiler
  • Collect sample data in local database (mongo?)
  • Interactive Krona plot
  • Only visualisation, no calculations

Follow-up actions

  • Stockholm creates a initial feature list based on their clinical micro needs
  • Share with all other nodes as a starting point for local needs
  • All nodes try to append/feedback to the feature wish list
  • Reconvene in a new meeting in a few weeks to share results
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