update after UM cyberattack

[Egon Willighagen]

Hi everyone,

our BiGCaT servers are still disconnected from the internet. Tina and I are doing our best to see what we can do, but we have started implementing our backup plans. It seems unlikely our servers will be back online soon

So, this update details a bit more of what I have in mind for Plan B.

1. the webservice

The webservice actually moved outside Maastricht University (UM) network last autumn, allowing us to gain experience with the Amazon WS. However, the Swagger documentation that users were presented with when opening webservice.bridgedb.org was not hosted on the same AWS system, but still here at BiGCaT. So, using the webservice continued to work, but the documentation not. As of last night, Plan B is well on its way, and https://bridgedb.github.io/swagger/ provides the documentation. In fact, it's a slight upgrade and using a more recent Swagger JavaScript library. The redirect still has to be put in place.

2. the Derby files

Here, I propose a change of working. All Derby files will be archived from now on, on Zenodo, Figshare, or possibly a institutional repository (or a combination of that). We have been doing this for metabolite identifiers and positive experiences. 

However, there are downstream users of the download folders on pathvisio.org/bridgedb.org (same folder, but accessible via two domains), such as the Bioconductor package. We do not have a Plan B for this, but I'm exploring how much we can do by using GitHub pages to contain indices that point to the aforementioned archives. This will need to be coordinated with downstream users. (This email is the start of that discussion.)

3. the BridgeDb website

The website is being migrated to GitHub pages. A lot of content needs to be ported (which is tricky, because the webserver hosting bridgedb.org is not connected to the internet), but a start is here: https://bridgedb.github.io/

Intention to have this operational before the end of the week, and have bridgedb.org redirect to this page.

4. BridgeDb Java library updates

I have a few PRs lined up. I will look at them asap, but I hope you understand we have had quite some emergency ICT work to do.

I hope this gives some insight in our progress and again apologize for the inconvenience. There is plenty of information about the CyberAttack, but the effects of this have not played out yet.

Egon

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E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
ORCID: 0000-0001-7542-0286
ImpactStory: https://impactstory.org/u/egonwillighagen

[Gray, Alasdair J G]

Egon,

Thanks for the update. It sounds like a reasonable approach going forward.

Let us know if there is anything we (Petros) can do to help.

Alasdair

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Alasdair J G Gray

Associate Professor in Computer Science, 
School of Mathematical and Computer Sciences 
Heriot-Watt University, Edinburgh, UK.

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[Egon Willighagen]

Hi all,

Following up on one of the points earlier this morning:

On Thu, Feb 13, 2020 at 8:26 AM Egon Willighagen <egon.wil...@gmail.com> wrote:

2. the Derby files

Here, I propose a change of working. All Derby files will be archived from now on, on Zenodo, Figshare, or possibly a institutional repository (or a combination of that). We have been doing this for metabolite identifiers and positive experiences. 

However, there are downstream users of the download folders on pathvisio.org/bridgedb.org (same folder, but accessible via two domains), such as the Bioconductor package. We do not have a Plan B for this, but I'm exploring how much we can do by using GitHub pages to contain indices that point to the aforementioned archives. This will need to be coordinated with downstream users. (This email is the start of that discussion.)

I have experimented with GitHub pages and can unfold a Plan B:

I have set up a "data" repository which contains an "gene_database/readme.md" which lists links to Figshare files (metabolites + interactions, bc the genes derby files are not archived yet). The Markdown is very trivial, and the content can be autogenerated later, e.g. from a list of DOIs. If we make the script a bit clever, it will use the metadata to figure out what the most recent versions are (based on the data), which ones are gene, metabolite, etc (we may have to use some keywords), and isolate the current ones and use the rest for the /archive/ subfolder (follow Nuno's most recent (autumn) proposal).

All, what do you think?

Check out: https://bridgedb.github.io/data/gene_database/

(if you start with http://bridgedb.org/data/gene_database/ you end up in the right location too, but not with https yet)

Egon