From 17c698f29742cbd24bdbf79e613a0124fce20316 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Sun, 24 May 2020 11:28:09 -0500 Subject: Edits --- doc/web/about.html | 107 +++++++++++++++++++++++++++------------------------ doc/web/about.org | 2 +- doc/web/download.org | 20 ++++++++++ 3 files changed, 78 insertions(+), 51 deletions(-) (limited to 'doc/web') diff --git a/doc/web/about.html b/doc/web/about.html index 1f8b1a1..ca0d952 100644 --- a/doc/web/about.html +++ b/doc/web/about.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + About/FAQ @@ -247,26 +247,26 @@ for the JavaScript code in this tag.

Table of Contents

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1 What is the 'public sequence resource' about?

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1 What is the 'public sequence resource' about?

The public sequence resource aims to provide a generic and useful @@ -277,25 +277,29 @@ sequence comparison and protein prediction.

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2 Who created the public sequence resource?

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2 Who created the public sequence resource?

The public sequence resource is an initiative by bioinformatics and -ontology experts who want to create something agile and useful for -the wider research community. The initiative started at the COVID-19 +ontology experts who want to create something agile and useful for the +wider research community. The initiative started at the COVID-19 biohackathon in April 2020 and is ongoing. The main project drivers are Pjotr Prins (UTHSC), Peter Amstutz (Curii), Michael Crusoe (Common -Workflow Language) and Thomas Liener (consultant, formerly EBI). But -as this is a free software initiative the project represents major -work by hundreds of software developers and ontology and data +Workflow Language), Thomas Liener (consultant, formerly EBI) and +Jerven Bolleman (Swiss Institute of Bioinformatics). +

+ +

+Notably, as this is a free software initiative, the project represents +major work by hundreds of software developers and ontology and data wrangling experts. Thank you everyone!

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3 How does the public sequence resource compare to other data resources?

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3 How does the public sequence resource compare to other data resources?

The short version is that we use state-of-the-art practices in @@ -314,8 +318,8 @@ public resources, including GISAID.

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4 Why should I upload my data here?

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4 Why should I upload my data here?

  1. We champion truly shareable data without licensing restrictions - with proper @@ -329,6 +333,9 @@ for bulk uploads
  2. There is no need to set up pipelines and/or compute clusters
  3. All workflows get triggered on uploading a new sequence
  4. When someone (you?) improves the software/workflows and everyone benefits
    5. +
  5. Your data gets automatically integrated with the Swiss Institure of +Bioinformatics COVID-19 knowledge base +https://covid-19-sparql.expasy.org/ (Elixir Switzerland)

@@ -340,8 +347,8 @@ multiple resources.

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5 Why should I not upload by data here?

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5 Why should I not upload by data here?

Funny question. There is no good reason not to upload your data here! @@ -354,8 +361,8 @@ data once and make the process smooth.

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6 How does the public sequence resource work?

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6 How does the public sequence resource work?

On uploading a sequence with metadata it will automatically be @@ -366,8 +373,8 @@ using workflows from the High Performance Open Biology Lab defined

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7 Is this about open data?

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7 Is this about open data?

All data is published under a Creative Commons 4.0 attribution license @@ -377,8 +384,8 @@ data and store it for further processing.

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8 Is this about free software?

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8 Is this about free software?

Absolutely. Free software allows for fully reproducible pipelines. You @@ -387,8 +394,8 @@ can take our workflows and data and run it elsewhere!

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9 How do I upload raw data?

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9 How do I upload raw data?

We are preparing raw sequence data pipelines (fastq and BAM). The @@ -403,8 +410,8 @@ assembly variations into consideration. This is all work in progress.

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10 How do I change metadata?

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10 How do I change metadata?

See the http://covid19.genenetwork.org/blog! @@ -412,8 +419,8 @@ See the http://covid19.genenetwork

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11 How do I change the work flows?

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12 How do I change the source code?

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12 How do I change the source code?

Go to our source code repositories, fork/clone the repository, change @@ -432,20 +439,20 @@ many PRs we already merged.

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13 How do I deal with private data and privacy?

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13 How do I deal with private data and privacy?

A public sequence resource is about public data. Metadata can refer to private data. You can use your own (anonymous) identifiers. We also plan to combine identifiers with clinical data stored securely at -REDCap. Contact Pjotr Prins if you want to work on this. +REDCap. See the relevant tracker for more information and contributing.

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14 Who are the sponsors?

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14 Who are the sponsors?

The main sponsors are listed in the footer. In addition to the time @@ -456,7 +463,7 @@ for donating COVID-19 related compute time.

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Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!
Modified 2020-05-24 Sun 10:26. +
Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!
Modified 2020-05-24 Sun 11:24.
diff --git a/doc/web/about.org b/doc/web/about.org index 26b675d..497b1b4 100644 --- a/doc/web/about.org +++ b/doc/web/about.org @@ -130,7 +130,7 @@ many PRs we already merged. A public sequence resource is about public data. Metadata can refer to private data. You can use your own (anonymous) identifiers. We also plan to combine identifiers with clinical data stored securely at -[[https://redcap-covid19.elixir-luxembourg.org/redcap/][REDCap]]. Contact Pjotr Prins if you want to work on this. +[[https://redcap-covid19.elixir-luxembourg.org/redcap/][REDCap]]. See the relevant [[https://github.com/arvados/bh20-seq-resource/issues/21][tracker]] for more information and contributing. * Who are the sponsors? diff --git a/doc/web/download.org b/doc/web/download.org index 498b132..c48b6d8 100644 --- a/doc/web/download.org +++ b/doc/web/download.org @@ -11,6 +11,10 @@ - [[#pangenome-browser-format][Pangenome Browser format]] - [[#log-of-workflow-output][Log of workflow output]] - [[#all-files][All files]] + - [[#planned][Planned]] + - [[#raw-sequence-data][Raw sequence data]] + - [[#multiple-sequence-alignment-msa][Multiple Sequence Alignment (MSA)]] + - [[#phylogenetic-tree][Phylogenetic tree]] * FASTA files @@ -67,3 +71,19 @@ Including in below link is a log file of the last workflow runs. * All files https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/ + +* Planned + +We are planning the add the following output (see also + +** Raw sequence data + +See [[https://github.com/arvados/bh20-seq-resource/issues/16][fastq tracker]] and [[https://github.com/arvados/bh20-seq-resource/issues/63][BAM tracker]]. + +** Multiple Sequence Alignment (MSA) + +See [[https://github.com/arvados/bh20-seq-resource/issues/11][MSA tracker]]. + +** Phylogenetic tree + +See [[https://github.com/arvados/bh20-seq-resource/issues/43][Phylo tracker]]. -- cgit v1.2.3