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.nojekyll

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search.json

@@ -6,6 +6,27 @@
     "section": "",
     "text": "something about the training we offer?\npoint to package docs?\npoint to package sciwiki pages?\npoint to external resources?"
   },
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+    "title": "Help",
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+    "text": "Depending on what kind of help you need, there are different resources you can consult:\n\nIf you would like to ask a question about any WILDS projects, do not hesitate to email us at wilds@fredhutch.org.\nIf you are a developer or you are familiar with GitHub, you can also open an issue on the GitHub repository that corresponds to the project you are interested in: https://github.com/getwilds/. For example, if you have an issue or question with the sixtyfour package, open an issue in the issue tracker for that project at https://github.com/getwilds/sixtyfour/issues.\nIf you are a member of our Slack organization, you are welcome to ask a question in our #general channel. If you are a Fred Hutch employee or you work for one of the organizations in the Cancer Consortium and you would like to join our Slack, please email us.\nSimilarly, if you are a Fred Hutch employee or you work for one of the organizations in the Cancer Consortium and you would like to have a face-to-face conversation please schedule a Data House Call and mention WILDS in the booking."
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+    "href": "help.html#we-would-be-happy-to-help-you-with-wilds",
+    "title": "Help",
+    "section": "",
+    "text": "Depending on what kind of help you need, there are different resources you can consult:\n\nIf you would like to ask a question about any WILDS projects, do not hesitate to email us at wilds@fredhutch.org.\nIf you are a developer or you are familiar with GitHub, you can also open an issue on the GitHub repository that corresponds to the project you are interested in: https://github.com/getwilds/. For example, if you have an issue or question with the sixtyfour package, open an issue in the issue tracker for that project at https://github.com/getwilds/sixtyfour/issues.\nIf you are a member of our Slack organization, you are welcome to ask a question in our #general channel. If you are a Fred Hutch employee or you work for one of the organizations in the Cancer Consortium and you would like to join our Slack, please email us.\nSimilarly, if you are a Fred Hutch employee or you work for one of the organizations in the Cancer Consortium and you would like to have a face-to-face conversation please schedule a Data House Call and mention WILDS in the booking."
+  },
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+    "href": "projects.html",
+    "title": "Projects",
+    "section": "",
+    "text": "R Packages\n\n\n\n\n\nrcromwell\n\nR client for interacting with Cromwell with WDL workflows\n\n\n\n\n\n\n\n\n\n\n\n\n\nsixtyfour\n\n🚚 CEO, entrepreneur\n\n\n\n\n\n\n\n\n\n\n\n\n\ncancerprof\n\nAPI Client for State Cancer Profiles\n\n\n\n\n\n\n\n\n\n\n\n\n\nproofr\n\nClient for the PROOF API\n\n\n\n\n\n\n\n\n\n\n\n\n\nbs\n\nBootstrap Components for DASL Projects\n\n\n\n\n\n\n\n\n\n\n\n\n\nrls\n\nRow Level Security Functions for PostgreSQL and Redshift\n\n\n\n\n\n\n\n\n\n\n\n\nPython Packages\nComing soon!\n\n\nDocker Recipes\n\n\n\n\n\nwilds-docker-library\n\nCentral location for all Docker containers associated with WILDS workflows\n\n\n\n\n\n\n\n\n\n\n\n\nResearch Compendia\nComing soon!\n\n\nWDLs\n\n\n\n\n\nww-sra-star\n\nWorkflow to download paired fastqs from SRA and pass through STAR 2 pass\n\n\n\n\n\n\n\n\n\n\n\n\n\nww-cell-ranger\n\nA basic starting point for a cell ranger workflow\n\n\n\n\n\n\n\n\n\n\n\n\n\nww-star-deseq2\n\nA demo repo to help folks run Star on RNA seq data and do DEseq2\n\n\n\n\n\n\n\n\n\n\n\n\n\nww-fastq-to-cram\n\nSelf-contained WDL workflow that converts a WGS FASTQ file into an unmapped CRAM file\n\n\n\n\n\n\n\n\n\n\n\n\nNextFlow\nComing soon!\n\n\nRepos status tally\n\n\n\n\n\n\n \n\n \n5\n\n\n\n\n\n\n\n \n\n \n2\n\n\n\n\n\n\n\n \n\n \n4"
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     "title": "Welcome to WILDS",
     "section": "",
     "text": "Open source software has allowed the biomedical data science community to flourish. 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. WILDS stands for Workflows Integrating Large Data and Software, which highlights our focus on people in their day-to-day scientific work. The mission of WILDS includes the following:\n\nEngage with the Cancer Consortium community about how they can adopt open science practices into their own workflows.\nEducate our community about the critical role that open source software plays in biomedical data science practice.\nSupport open source software developers across the Cancer Consortium.\nElevate the quality of open-source software being developed at Fred Hutch.\nEmpower new open-source developers by evangelizing best practices and catalyzing community around the open-source software development process.\nConnect developers, researchers, and providers to opportunities to share, academically publish, and publicize their software.\nCollaborate within the Fred Hutch community to build the next generation of open-source software tools.\n\n\n\n\nTo support our mission, WILDS is actively engaged in the following activities:\n\nWe maintain, distribute, and publish open source scientific software, mostly implemented in the Python and R ecosystems.\nWe maintain and distribute open source scientific workflows implemented in WDL or Nextflow.\nWe develop research compendia to demonstrate common data analyses and how they can best be organized and shared.\nWe package and develop Docker recipes and Dockerfiles so that researchers can run pipelines in consistent computing environments.\nWe create and maintain documentation about how to use and contribute to WILDS resources.\nWe co-sponsor and create materials for DaSL’s Community Studios.\n\nAll 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.\n\n\n\n\n\n\n\nR Packages\n\n\n\n\n\n\n\n\n\n\n\n\nPython Packages\n\n\n\n\n\n\n\n\n\n\n\n\nDocker Recipes\n\n\n\n\n\n\n\n\n\n\n\n\nResearch Compendia\n\n\n\n\n\n\n\n\n\n\n\n\nWDL Workflows\n\n\n\n\n\n\n\n\n\n\n\n\nNextflow Workflows"
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-    "title": "Projects",
-    "section": "",
-    "text": "R Packages\n\n\n\n\n\nrcromwell\n\nR client for interacting with Cromwell with WDL workflows\n\n\n\n\n\n\n\n\n\n\n\n\n\nsixtyfour\n\n🚚 CEO, entrepreneur\n\n\n\n\n\n\n\n\n\n\n\n\n\ncancerprof\n\nAPI Client for State Cancer Profiles\n\n\n\n\n\n\n\n\n\n\n\n\n\nproofr\n\nClient for the PROOF API\n\n\n\n\n\n\n\n\n\n\n\n\n\nbs\n\nBootstrap Components for DASL Projects\n\n\n\n\n\n\n\n\n\n\n\n\n\nrls\n\nRow Level Security Functions for PostgreSQL and Redshift\n\n\n\n\n\n\n\n\n\n\n\n\nPython Packages\nComing soon!\n\n\nDocker Recipes\n\n\n\n\n\nwilds-docker-library\n\nCentral location for all Docker containers associated with WILDS workflows\n\n\n\n\n\n\n\n\n\n\n\n\nResearch Compendia\nComing soon!\n\n\nWDLs\n\n\n\n\n\nww-sra-star\n\nWorkflow to download paired fastqs from SRA and pass through STAR 2 pass\n\n\n\n\n\n\n\n\n\n\n\n\n\nww-cell-ranger\n\nA basic starting point for a cell ranger workflow\n\n\n\n\n\n\n\n\n\n\n\n\n\nww-star-deseq2\n\nA demo repo to help folks run Star on RNA seq data and do DEseq2\n\n\n\n\n\n\n\n\n\n\n\n\n\nww-fastq-to-cram\n\nSelf-contained WDL workflow that converts a WGS FASTQ file into an unmapped CRAM file\n\n\n\n\n\n\n\n\n\n\n\n\nNextFlow\nComing soon!\n\n\nRepos status tally\n\n\n\n\n\n\n \n\n \n5\n\n\n\n\n\n\n\n \n\n \n2\n\n\n\n\n\n\n\n \n\n \n4"
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-    "text": "Depending on what kind of help you need, there are different resources you can consult:\n\nIf you would like to ask a question about any WILDS projects, do not hesitate to email us at wilds@fredhutch.org.\nIf you are a developer or you are familiar with GitHub, you can also open an issue on the GitHub repository that corresponds to the project you are interested in: https://github.com/getwilds/. For example, if you have an issue or question with the sixtyfour package, open an issue in the issue tracker for that project at https://github.com/getwilds/sixtyfour/issues.\nIf you are a member of our Slack organization, you are welcome to ask a question in our #general channel. If you are a Fred Hutch employee or you work for one of the organizations in the Cancer Consortium and you would like to join our Slack, please email us.\nSimilarly, if you are a Fred Hutch employee or you work for one of the organizations in the Cancer Consortium and you would like to have a face-to-face conversation please schedule a Data House Call and mention WILDS in the booking."
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-    "title": "Help",
-    "section": "",
-    "text": "Depending on what kind of help you need, there are different resources you can consult:\n\nIf you would like to ask a question about any WILDS projects, do not hesitate to email us at wilds@fredhutch.org.\nIf you are a developer or you are familiar with GitHub, you can also open an issue on the GitHub repository that corresponds to the project you are interested in: https://github.com/getwilds/. For example, if you have an issue or question with the sixtyfour package, open an issue in the issue tracker for that project at https://github.com/getwilds/sixtyfour/issues.\nIf you are a member of our Slack organization, you are welcome to ask a question in our #general channel. If you are a Fred Hutch employee or you work for one of the organizations in the Cancer Consortium and you would like to join our Slack, please email us.\nSimilarly, if you are a Fred Hutch employee or you work for one of the organizations in the Cancer Consortium and you would like to have a face-to-face conversation please schedule a Data House Call and mention WILDS in the booking."
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