From 9c7f23273ef2d04c7ecbb9333a09e32c556d52d2 Mon Sep 17 00:00:00 2001 From: seankross Date: Tue, 26 Mar 2024 10:05:29 -0700 Subject: [PATCH 1/4] added some content --- index.qmd | 35 ++++++++++++++++++++++++++--------- 1 file changed, 26 insertions(+), 9 deletions(-) diff --git a/index.qmd b/index.qmd index 0e94f04..beeca80 100644 --- a/index.qmd +++ b/index.qmd @@ -26,15 +26,19 @@ cat("{{< fa box-open >}} ") ### The Open Source Software Office of the Fred Hutchinson Cancer Center -#### Our Missions - -In regocnition of ther fact that open source software is the engine of -biomedical data science, the Data Science Lab (DaSL) created WILDS, the open -source software office of the Fred Hutch Cancer Center. The mission of WILDS -includes the following: - -- Engage with people developing open-source software across the Cancer -Consortium. +#### Our Mission + +Open source software has allowed the biomedical data science community to +flourish, and therefore to encourage open science practices and to cultivate +the development of open source software at Fred Hutch, the Data Science Lab +(DaSL) created WILDS, the open source software office of the Fred Hutch Cancer +Center. The mission of WILDS includes the following: + +- Engage with the Cancer Consortium community about how they can adopt open +science practices into their own workflows. +- Educate our community about the critical role that open source software plays +in biomedical data science practice. +- Support open-source software developers across the Cancer Consortium. - Elevate the quality of open-source software being developed at Fred Hutch. - Empower new open-source developers by evangelizing best practices and catalyzing community around the open-source software development process. @@ -43,6 +47,18 @@ academically publish, and publicize their software. - Collaborate within the Fred Hutch community to build the next generation of open source software tools. +#### Our Contribution + +To support our mission, WILDS is actively engaged in the following activities: + +- We maintain, distribute, and publish open source scientific software, mostly +implemented in the Python and R ecosystems. +- We maintain and distribute open source scientific workflows implemented in +WDL or Nextflow. These workflows are designed for researchers to either use +off-the-shelf or as templates that they can adapt into their own work. +- +- We co-sponsor and create materials for [DaSL's Community Studios][comm]. +

{{< include cards.qmd >}} @@ -69,3 +85,4 @@ layout_column_wrap( [dasl]: https://hutchdatascience.org/ [guide]: https://getwilds.org/guide/ +[comm]: https://hutchdatascience.org/communitystudios/ \ No newline at end of file From 9106b5da988b5d9590fb53e812014c6b644ecb90 Mon Sep 17 00:00:00 2001 From: seankross Date: Thu, 28 Mar 2024 09:31:21 -0700 Subject: [PATCH 2/4] added yet more content --- cards.qmd | 2 +- index.qmd | 20 +++++++++++++++----- 2 files changed, 16 insertions(+), 6 deletions(-) diff --git a/cards.qmd b/cards.qmd index 36716c8..dcba7e7 100644 --- a/cards.qmd +++ b/cards.qmd @@ -1,4 +1,4 @@ -```{r echo=FALSE, results="asis", message=FALSE} +```{r echo=FALSE, results="asis", message=FALSE, warning=FALSE} library(bslib) library(htmltools) library(glue) diff --git a/index.qmd b/index.qmd index beeca80..da26f00 100644 --- a/index.qmd +++ b/index.qmd @@ -54,12 +54,21 @@ To support our mission, WILDS is actively engaged in the following activities: - We maintain, distribute, and publish open source scientific software, mostly implemented in the Python and R ecosystems. - We maintain and distribute open source scientific workflows implemented in -WDL or Nextflow. These workflows are designed for researchers to either use -off-the-shelf or as templates that they can adapt into their own work. -- +WDL or Nextflow. +- We develop [research compendia][rescomp] to demonstrate common data analyses +and how they can best be organized and shared. +- We package and develop Docker recipies and Dockerfiles so that researchers +can run pipelines in consistent computing environments. +- We create and maintain documentation about how to use and contribute to +WILDS resources. - We co-sponsor and create materials for [DaSL's Community Studios][comm]. -

+All of these open source resources are designed for researchers to either use +off-the-shelf or as tools and templates that they can adapt into their own work. +Click on any of the boxes below to explore the resources that WILDS has to +offer. + + {{< include cards.qmd >}} @@ -85,4 +94,5 @@ layout_column_wrap( [dasl]: https://hutchdatascience.org/ [guide]: https://getwilds.org/guide/ -[comm]: https://hutchdatascience.org/communitystudios/ \ No newline at end of file +[comm]: https://hutchdatascience.org/communitystudios/ +[rescomp]: https://research-compendium.science/ \ No newline at end of file From 77fab3c63e5d23bbfe81f6268d7c82a9068c1c82 Mon Sep 17 00:00:00 2001 From: seankross Date: Thu, 28 Mar 2024 11:51:20 -0700 Subject: [PATCH 3/4] changed mention of packages to projects --- _quarto.yml | 2 +- cards.qmd | 12 ++++++------ index.qmd | 2 +- packages.qmd => projects.qmd | 4 ++-- 4 files changed, 10 insertions(+), 10 deletions(-) rename packages.qmd => projects.qmd (97%) diff --git a/_quarto.yml b/_quarto.yml index 51b27d0..b9a4012 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -10,7 +10,7 @@ website: left: - href: index.qmd text: Home - - packages.qmd + - projects.qmd #- learn.qmd - help.qmd - getinvolved.qmd diff --git a/cards.qmd b/cards.qmd index dcba7e7..0114ccb 100644 --- a/cards.qmd +++ b/cards.qmd @@ -21,7 +21,7 @@ card_r <- card( ), c_image( file = "assets/Rlogo.svg", - href = "packages.html#r-packages" + href = "projects.html#r-packages" ) ) card_python <- card( @@ -31,7 +31,7 @@ card_python <- card( ), c_image( file = "assets/Pythonlogo.svg", - href = "packages.html#python-packages" + href = "projects.html#python-packages" ) ) card_docker <- card( @@ -41,7 +41,7 @@ card_docker <- card( ), c_image( file = "assets/docker-mark-blue.png", - href = "packages.html#docker" + href = "projects.html#docker" ) ) card_comp <- card( @@ -52,7 +52,7 @@ card_comp <- card( c_image( # from research-compendium.github.io file = "assets/rc-logo.svg", - href = "packages.html#research-compendia", + href = "projects.html#research-compendia", max_width = "88%" ) ) @@ -63,7 +63,7 @@ card_wdl <- card( ), c_image( file = "assets/WDLlogo.png", - href = "packages.html#wdls" + href = "projects.html#wdls" ) ) card_nf <- card( @@ -73,7 +73,7 @@ card_nf <- card( ), c_image( file = "assets/nf-logo.png", - href = "packages.html#nextflow" + href = "projects.html#nextflow" ) ) ``` diff --git a/index.qmd b/index.qmd index da26f00..0013571 100644 --- a/index.qmd +++ b/index.qmd @@ -88,7 +88,7 @@ layout_column_wrap( {{< fa circle-info >}} **Read** - [WILDS Contributor Guide][guide] -{{< fa hammer >}} **Contribute** - See our [packages page](packages.html) +{{< fa hammer >}} **Contribute** - See our [projects page](projects.html) diff --git a/packages.qmd b/projects.qmd similarity index 97% rename from packages.qmd rename to projects.qmd index 92ffe5a..277a256 100644 --- a/packages.qmd +++ b/projects.qmd @@ -1,8 +1,8 @@ --- -title: "Packages" +title: "Projects" --- -## WILDS Packages +## WILDS Projects ```{r include=FALSE} library(glue) From 53ec5fa4c4c2c44cf817de58ed96dbf509a6d391 Mon Sep 17 00:00:00 2001 From: seankross Date: Mon, 1 Apr 2024 17:24:31 -0700 Subject: [PATCH 4/4] added more content --- getinvolved.qmd | 21 ++++++++++++++++----- help.qmd | 17 ++++++++++++++--- 2 files changed, 30 insertions(+), 8 deletions(-) diff --git a/getinvolved.qmd b/getinvolved.qmd index 6572a28..778e3a3 100644 --- a/getinvolved.qmd +++ b/getinvolved.qmd @@ -1,18 +1,29 @@ --- title: "Get Involved" +toc: false --- ## DASL Guide -The [WILDS Contributor Guide][guide] is the home for resources and best practices for WDL and Nextflow workflows, research compendia, Docker files and software. - -In addition, the guide outlines the best practices that we strive to follow while developing WILDS. +We maintain the [WILDS Contributor Guide][guide] as a collection of guidelines, +review criteria, and best practices for developing production-ready WDL and +Nextflow workflows, research compendia, Docker files and software. +Our goal in developing the WILDS Contributor Guide is not just limitted to the +care and keeping of WILDS, we hope it can serve as a model for research or +software development groups in terms of how they think about code and software +quality. ## Make a contribution -If you would like to make a contribution to any DaSL WILDS products please open a pull request in the respective GitHub repository. For example, if you want to make a contribution to the [sixtyfour][] package, open a pull request in the repository for that package at . +If you would like to make a contribution to any DaSL WILDS projects please open +a pull request in the appropriate GitHub repository. For example, if you want to +make a contribution to the [sixtyfour][six] package, open a pull request in +the repository for that package at . + +If you are interested in making another kind of contribution, we would be happy +to chat. Please contact us at `wilds@fredhutch.org`. [guide]: https://getwilds.org/guide/ -[sixtyfour]: https://github.com/getwilds/sixtyfour/ +[six]: https://github.com/getwilds/sixtyfour/ diff --git a/help.qmd b/help.qmd index d17a9cf..ea9df8d 100644 --- a/help.qmd +++ b/help.qmd @@ -1,12 +1,23 @@ --- title: "Help" +toc: false --- -## Report a problem/ask a question/etc +## Report a problem with one of our projects -If you have a problem with any DaSL WILDS products please open an issue in the respective GitHub repository. For example, if you have an issue or question with the [sixtyfour][] package, open an issue in the issue tracker for that package at . +If you have a problem with any DaSL WILDS projects please open an issue in the +respective GitHub repository. For example, if you have an issue or question +with the [sixtyfour][six] package, open an issue in the issue tracker for that +package at . +## Get help using WILDS +We are always happy to chat if you contact us at `wilds@fredhutch.org`. If you +are a Fred Hutch employee or you work for one of the organizations in the +[Cancer Consortium][ccon] please schedule a [Data House Call][dhc] and mention +WILDS in the booking. -[sixtyfour]: https://github.com/getwilds/sixtyfour/ +[six]: https://github.com/getwilds/sixtyfour/ +[ccon]: https://www.cancerconsortium.org/ +[dhc]: https://hutchdatascience.org/datahousecalls/