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    luke
    @luke-c-sargent
    @/all heyo, first post is a request for review of the doc/roadmap by folks planning to do development tasks; what you’d be interested in working on, what could be broken down more, what does or does not make sense, etc — per my pledge in the meeting, i’d like to get prelimenary assignments done soon
    ‘borrowing’ from the AnVIL group’s approach, i’m going through the board now and tagging folks who will be or are already involved in tasks, but feel free to edit as desired
    luke
    @luke-c-sargent
    for many if not most of these, there will be multiple names, so i’ve tagged myself on most of them but that doesn’t mean i’m task-hoarding
    StefaniaMontesinos
    @StefaniaMontesinos
    Hi, I'm interested in this working group. Can you please give more information about it?
    Vahid
    @VJalili
    Thank you for your interest. You may find some high-level information in the following document. https://docs.google.com/document/d/15D5NddEOzYtsZwu6rzTA4Vu2deU0dLX63Pn-DkgumGE/edit?usp=sharing
    StefaniaMontesinos
    @StefaniaMontesinos
    Can you please give me access to the google drive file?
    luke
    @luke-c-sargent
    drat, i should have made it public :( switching now, i’ll ping you when it’s ready
    @StefaniaMontesinos it should work now
    StefaniaMontesinos
    @StefaniaMontesinos
    Yes, I have access. Thank you! What I should do next for be on the working group? Or I just connect to the zoom call?
    luke
    @luke-c-sargent
    hooray! yes, joining our calls will be the best way to stay current, and keeping an eye on this channel for developments
    Christophe Antoniewski
    @drosofff
    Hi @luke-c-sargent I am joining the channel after bouncing off the public health channel. I was not aware of these Galaxy Working Groups, it's promising. I would be glad to contribute. We are developing analysis workflows for Acute Myeloid Leukemia sequencing data and for single cell RNAseq analysis of Glioblastoma
    luke
    @luke-c-sargent
    hello @drosofff (of GalaxyKickstart fame!) — cool deal, welcome! we are still in the early phases of cancer-centric galaxy work, investigating various angles like cloud resource management, protected dataset access, and testing Oregon Health and Science University’s multiplex whole-tissue imaging/analysis pipelines. Part of our goal is collecting tools and workflows for other cancer data analyses, so enabling workflows such as yours is very much on our roadmap
    Helena Rasche
    @hexylena:matrix.org
    [m]
    Hey all, fyi Saskia Hiltemann and I are working on some cancer tools, but not the infrastructure, so cool to see the work going on here :)
    Jeremy Goecks
    @jgoecks
    @hexylena:matrix.org Can you share a bit about what you're doing that's related to cancer? It would be great to coordinate efforts more.
    @drosofff I'd like to hear more about what you're doing in this space. Do you have anything you can share with us about your progress so far? We're also ramping up sc-RNA-seq work in cancer—perhaps we could work together on this? I've thought about trying to build on the workflows in place at https://humancellatlas.usegalaxy.eu/
    Helena Rasche
    @hexylena:matrix.org
    [m]
    The current priority for us is getting https://github.com/morinlab/tools-morinlab updated and in IUC.
    Jeremy Goecks
    @jgoecks
    Why these tools?
    Helena Rasche
    @hexylena:matrix.org
    [m]
    We want a cancer galaxy that supports a wide range of analyses and reproductions. Not all of those, some of them are just outdated or can be superseded by others, but we're looking to make an inventory amongst our researchers of their needs to augment this list, but this was our starting point.
    We've got a number of cancer datasets and analysis projects ongoing but since we run an in-house galaxy without access to these US data resources we're mostly focused on the tools portion that supports our researchers
    Jeremy Goecks
    @jgoecks
    Thanks for the additional context. These tools are pretty old and, at least for U.S. researchers, not especially relevant anymore. Agree it would be good to make a list of tools/datasets that would be useful to have in Galaxy, but it seems that starting with the analysis needs first makes sense. For instance, we need a somatic mutation calling pipeline; GATK is a great starting point for best practice approaches here rather than strelka/pindel. https://github.com/ohsu-comp-bio/compbio-galaxy-wrappers/tree/master/gatk Aside: I think that Dave B from Penn State was working on GATK at one point as well.
    Christophe Antoniewski
    @drosofff
    hi @jgoecks we are working a lot on somatic varscan. in replacement of GATK. But if there was a refreshed GATK wrapper I would consider it of course. happy to contribute to fixes on both wrappers in any case
    Unfortunately, right now I am fighting with uwsgi after a py2 -> py3 update on our dev server. And it sucks ;-)
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    Helena Rasche: regarding the Morin Lab tools: strelka is wrapped and in tools-iuc, and I have an open iuc PR for manta, which requires quite some additional work.
    In general, I'm very interested in Galaxy WFs for somatic/germline variant calling from cancer samples.
    https://github.com/AG-Boerries/MIRACUM-Pipe-Galaxy is a good starting point if you want to familiarize yourself with the WFs I'm developing (as the usegalaxy.eu team's contribution to a Germany-wide initiative to provide University hospitals with an analysis pipeline to support Molecular Tumor Boards).
    Helena Rasche
    @hexylena:matrix.org
    [m]
    Thanks wm75 (Wolfgang Maier) ! we've been using the IUC version of strelka already and yeah, no complaints. And thanks for sharing the MIRACUM pipelines, hadn't seen that but remember you talking about the project a lot :) Hopefully we'll get some workflows together from our end shortly as well.
    Saskia Hiltemann
    @shiltemann:matrix.org
    [m]
    @jgoecks: sure, I've been out of the cancer field for a while, but point is we remembered this work from morin lab, and wanted to create a modern version of it, a "Cancer Galaxy" flavour, similar to the NanoGalaxy we made, i.e. a large suite of tools, workflows, and supporting training materials. We figured we would start by taking inventory of the morinlab tools, see which ones are still relevant and bring those up to IUC standards. We would be happy if you / this group can suggest additional current tools/workflows that would be good to include here, that are either already in Galaxy, or that would be nice to bring in, etc. Our group is currently focused on machine learning approaches, classification etc, but we want to offer a broad range of tools and workflows for different types of cancer analyses. Maybe we can keep create a table of tools/workflows we want or already have for such a Galaxy flavour?
    wm75 (Wolfgang Maier) cool @ wrappers and MIRACUM, we should definitely collaborate on ths :+1:
    Christophe Antoniewski
    @drosofff
    :+1: @shiltemann:matrix.org
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    Saskia Hiltemann: looking forward to it 👍️
    Jeremy Goecks
    @jgoecks
    Thanks all for the great discussion. @shiltemann:matrix.org : your "Cancer Galaxy" vision matches mine and likely what others are thinking as well. Some additional things in addition to tools/workflows/training materials that would be nice are (1) making it easy to import cancer datasets that are useful/needed for analyses and (2) workflow reports. @/all Could we attempt to index our collective work and, best case, coordinate a bit? Perhaps use IUC and IWC for some of our workflows, a Github issue/repo to track our work, and a hub page to list everything?
    Jeremy Goecks
    @jgoecks
    In addition to the bulk omics work it sounds like many are working on, my group is particularly interested in single-cell spatial methods omics and multiplex tissue imaging as well as machine learning and creating databases of associations b/t molecular signatures and response/resistance
    While I'm thinking about coordination, it would be great to set up some work through the CoFest at GCC 2021. @luke-c-sargent perhaps you could lead the charge from the U.S. side? @wm75:matrix.org
    Christophe Antoniewski
    @drosofff

    Perhaps use IUC and IWC for some of our workflows, a Github issue/repo to track our work, and a hub page to list everything?

    IWC stands for what @jgoecks ?
    Is is something like MIRACUM that you are considering ? I find it nice. In any case I agree that the GitHub option is a must, to me at list.

    On another line, I forgot to mention that there are a couple of other topics very important to us: CNVs, mutational signatures (Cosmic as well as others like the BRCAness, etc), and local variant databases for specific project with elastic search for efficient indexing. On single cell RNAseq side, we find the UCSC cell browser super cool and integrating it into Galaxy (at least as UCSC tables are) would be nice.

    Saskia Hiltemann
    @shiltemann:matrix.org
    [m]
    @jgoeks absolutely @ reports, I've got a couple of groups still relliant on iReports in workflows but want to move that completely to workflow reports. Regarding import of datasets we are/will be working on integrating EGA, beacons etc
    Jeremy Goecks
    @jgoecks

    @drosofff

    IWC stands for what @jgoecks ?

    Intergalactic Workflow Commission (https://github.com/galaxyproject/iwc), similar to the IUC but for workflows

    Is is something like MIRACUM that you are considering ? I find it nice. In any case I agree that the GitHub option is a must, to me at list.

    This is nice and a great start. I imagine something associated with the Galaxy training network as well (https://training.galaxyproject.org/)

    On single cell RNAseq side, we find the UCSC cell browser super cool and integrating it into Galaxy (at least as UCSC tables are) would be nice.

    The UCSC cell browser is integrated with Galaxy, see workflows on https://humancellatlas.usegalaxy.eu/ for example. FYI, I'm a big fan of cellxgene, which is also integrated with Galaxy

    Jeremy Goecks
    @jgoecks

    @shiltemann:matrix.org

    integrating EGA, beacons etc

    EGA meaning open datasets or also protected datasets?
    Beacons meaning GAG4H?

    We're working to connect Galaxy with the NCI Cancer Research Data Commons to get access to all the datasets in there (https://datacommons.cancer.gov/)

    4 replies
    Christophe Antoniewski
    @drosofff
    Hi @jgoecks you mentioned cellxgene integration in Galaxy. It is not in the toolshed. Is there an Interactive tool somewhere in a GitHub ?
    2 replies
    tnabtaf
    @tnabtaf:matrix.org
    [m]
    Hi All, The bioinformatics MS program at the University of Oregon is looking for projects for student teams to work on this coming academic year. If you have any project ideas, then I encourage you to submit them. (Alex Ostrovsky came out of this program and can answer questions about it.)