How to give data back

[dawe]

Hi all,
I'm dealing with a "data delivery" issue in our Illumina facility.
Essentially I would like to know how you deal with giving results back to researchers?
I'm possibly ok with ChIP-seq data, but I would like to know how you deliver resequencing results (and SNP calling)...

d

[westerman]

Deliver? Via web interface. Yes, perhaps not the most efficient transport method but it is universal and people don't seem to mind letting their browsers download for hours. Although I did once put the customer's data on a mini-hard-drive. But since I need to keep a copy of the data it is also available via the web.

Pipeline the results? Still working on that problem. Each project seems to be a bit different.

[dawe]

Deliver? Via web interface. Yes, perhaps not the most efficient transport method but it is universal and people don't seem to mind letting their browsers download for hours. Although I did once put the customer's data on a mini-hard-drive. But since I need to keep a copy of the data it is also available via the web.

Pipeline the results? Still working on that problem. Each project seems to be a bit different.

Yep... I found IGV network capabilities quite interesting for ChIP-seq, and also bigWig/bigBed formats... Still thinking about resequencing...

[ScottC]

We deliver our results using either a web delivery system or DVD, unless raw and intermediate data is requested, in which case we deliver on an external HDD. Most of our data is one or two lanes of sequencing data, though.

[robhall]

We here at UW-Seattle host an sFTP site

[agagne]

We distribute text files via an ftp server, larger files we send out on external hard drives.

[r.c]

You can use Galaxy Sample Tracking at your facility and use its in-built data transfer utility to make datasets available to the customers.

[elaney_k]

You can use Galaxy Sample Tracking at your facility and use its in-built data transfer utility to make datasets available to the customers.

How secure is data that's uploaded through the Galaxy interface?

[fubar]

How secure is data that's uploaded through the Galaxy interface?

(I'm a Galaxy developer so my views are probably biased)

Short answer: Security is a complex issue and there are no simple short answers other than from marketing droids...

Longer answer: There are at least three security issues to think about - the front end web server, traffic to and from the application and Galaxy itself.

The public Galaxy server uses http - I would not consider that secure although (see below) once data is uploaded and assuming the user has set restrictive permissions, it's secured from access by other, unauthorized Galaxy users (unless they packet sniffed your password!)

If we're talking about a private deployment of a Galaxy instance competently configured and locked down behind a secure https web server, then unauthorized Galaxy access is going to be really hard to get for starters.

Once someone gains access to Galaxy itself, the application has inbuilt RBAC so an individual dataset can be locked down to a user or group of users easily and flexibly. Permissions on a dataset propagate to derived datasets as the default. Finally, the developers have always taken security very seriously and the code protects against all the commonest web security threats that we know about - like session key hashed url paths eg

Galaxy source has never been formally audited for security - but at least you can take a look for yourself to see what weaknesses there might be. Please let us know if you do manage to find anything we need to know about!