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authorPeter Amstutz2020-08-05 16:06:11 -0400
committerGitHub2020-08-05 16:06:11 -0400
commitfdb1b012fc04ee07f401541e181e28fe442c9454 (patch)
tree8486db1087692dffcea9d93814e436d9cf150b47 /doc/web/about.org
parent86f31ef60f65a820bf9ac25c3fc01c88f2a9ebfe (diff)
parent2d20bf90497588a297ca98a78ee0fbbcadf95569 (diff)
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Merge pull request #99 from AndreaGuarracino/patch-2
several fixes in the website, added links to video talk and poster, new pangenome generation workflow
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@@ -17,7 +17,10 @@
- [[#how-do-i-change-the-work-flows][How do I change the work flows?]]
- [[#how-do-i-change-the-source-code][How do I change the source code?]]
- [[#should-i-choose-cc-by-or-cc0][Should I choose CC-BY or CC0?]]
+ - [[#are-there-also-variant-in-the-RDF-databases]][Are there also variant in the RDF databases?]
- [[#how-do-i-deal-with-private-data-and-privacy][How do I deal with private data and privacy?]]
+ - [[#do-you-have-any-checks-or-concerns-if-human-sequence-accidentally-submitted-to-your-service-as-part-of-a-fastq][Do you have any checks or concerns if human sequence accidentally submitted to your service as part of a fastq?]
+ - [[#does-PubSeq-support-only-SARS-CoV-2=data]][Does PubSeq support only SARS-CoV-2 data?]
- [[#how-do-i-communicate-with-you][How do I communicate with you?]]
- [[#who-are-the-sponsors][Who are the sponsors?]]
@@ -28,6 +31,8 @@ resource for COVID-19 research. The focus is on providing the best
possible sequence data with associated metadata that can be used for
sequence comparison and protein prediction.
+We were at the *Bioinformatics Community Conference 2020*! Have a look at the [[https://bcc2020.sched.com/event/coLw]][video talk] ([[https://drive.google.com/file/d/1skXHwVKM_gl73-_4giYIOQ1IlC5X5uBo/view?usp=sharing]][alternative link]) and the [[https://drive.google.com/file/d/1vyEgfvSqhM9yIwWZ6Iys-QxhxtVxPSdp/view?usp=sharing]][poster].
+
* Who created the public sequence resource?
The *public sequence resource* is an initiative by [[https://github.com/arvados/bh20-seq-resource/graphs/contributors][bioinformatics]] and
@@ -171,6 +176,12 @@ because we know people like the attribution clause.
In all honesty: we prefer both data and software to be free.
+* Are there also variant in the RDF databases? *
+
+We do output a RDF file with the pangenome built in, and you can parse it because it has variants implicitly.
+
+We are also writing tools to generate VCF files directly from the pangenome.
+
* How do I deal with private data and privacy?
A public sequence resource is about public data. Metadata can refer to
@@ -178,6 +189,15 @@ 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]]. See the relevant [[https://github.com/arvados/bh20-seq-resource/issues/21][tracker]] for more information and contributing.
+* Do you have any checks or concerns if human sequence accidentally submitted to your service as part of a fastq? *
+
+We are planning to remove reads that match the human reference.
+
+* Does PubSeq support only SARS-CoV-2 data? *
+
+To date, PubSeq is a resource specific to SARS-CoV-2, but we are designing it to be able to support other species in the future.
+
+
* How do I communicate with you?
We use a [[https://gitter.im/arvados/pubseq?utm_source=share-link&utm_medium=link&utm_campaign=share-link][gitter channel]] you can join.