Freezer status metadata

[antgonza]

(from Rob) It would be REALLY useful to be able to detect which samples we had dna and/or physical specimen left over in the freezer.

[adamrp]

There is already a "has_physical_specimen" field in the required_sample_info table; does that suffice, or do we also need a "has_dna" field? Is this a question for the wet lab folks?

[rob-knight]

Need both

On Sep 15, 2014, at 1:42 PM, "adamrp" <notifications@github.commailto:notifications@github.com> wrote:

There is already a "has_physical_specimen" field in the required_sample_info table; does that suffice, or do we also need a "has_dna" field? Is this a question for the wet lab folks?

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/5#issuecomment-55646848.

[wasade]

We also need an easy way for people to update that field otherwise it could
easily get out of sync
Need both

On Sep 15, 2014, at 1:42 PM, "adamrp" <notifications@github.com<mailto:
notifications@github.com>> wrote:

There is already a "has_physical_specimen" field in the
required_sample_info table; does that suffice, or do we also need a
"has_dna" field? Is this a question for the wet lab folks?

—
Reply to this email directly or view it on GitHub<
https://github.com/biocore/qiita/issues/5#issuecomment-55646848>.

—
Reply to this email directly or view it on GitHub
#5 (comment).

[ackermag]

This could be tracked in the mapping file we receive from the wetlab so that it is available for upload to prep. Problems occur when subsets of study samples are used for e.g. primer testing or retrieved for collaborations e.g. family study samples for Blastocystis collaboration. We will have to estimate remaining dna volume (some is lost in aliquoting repeatedly).

[ackermag]

In the wetlab there should be a log of samples available - primary sample and primary dna (we usually discard the amplicons. We should also track the freezer location/inventory.

[antgonza]

How do we want to deal with this? These are not required fields for any of the templates and it sounds more like a standard that we want to impose in the template generation (perhaps in the weblab) and not in Qiita.

[josenavas]

I think this should be move to the labadmin project - qiita is not a labadmin site to deal how our freezers are organized.

[ackermag]

This will be fairly easy to track for studies sequenced by us in the wetlab
but will not be generally available. Right now I usually assume that the
physical specimen is not available unless it is AGP (potentially available)
or a study I am familiar with (like Jess M soils) where I know there is
physical specimen. Many times we have to return the specimen to the
collaborator and have no knowledge of what happens to it.

On Mon, Oct 12, 2015 at 9:09 AM, Antonio Gonzalez notifications@github.com
wrote:

How do we want to deal with this? These are not required fields for any of
the templates and it sounds more like a standard that we want to impose in
the template generation (perhaps in the weblab) and not in Qiita.

—
Reply to this email directly or view it on GitHub
#5 (comment).

Gail Ackermann
Knight Lab
UCSD
glackermann@ucsd.edu ackermag@ucsd.edu

[antgonza]

From your replies it sounds like we can close as it's not longer within the scope of the template validations. Please, reopen if you think otherwise.