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Study protocol questions

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Study protocol questions mlifton  2007-11-07 10:12
Status: Closed
 
Hi Matt and Sarah,
 
I've been playing around on our server and trying to set up a simple study that is already in progress as a means of figuring out this whole system. It is Barouch\07-06. I noticed a few things that need tweaking for animal studies. I know that there are changes in 2.3 as far as animal studies, so I realize that these items may already be improved in 2.3. Here goes:
 
1) In the study protocol definition under assays when you define a new assay the material required section does not allow you to add to the drop down menus. Right now I have the requirements set as 0.5 ml PBMC, but I'd really like it to say something like 0.5ml lysed whole blood.
 
2) In the assay schedule it would be nice to be able to either import a schedule or be able to define multiple timepoints. In animal studies we have many more timepoints than in human studies. I might have seen some way to import this, but I have no idea how I got there ~or even if that's what it really was.
 
I hope to add the flow areas next week. It's really simple analysis that won't need any compensation, very few gate adjustments, and well defined results that we're interested in.
 
Thanks,
 
Michelle
 
 
marki responded:  2007-11-07 12:37
Hi Michelle,

It sounds like you are using the protocol designer to define a study protocol. What usually happens is that after the protocol is designed you create a "Study Folder" to store all the data collected in the study.

So in answer to your questions
1) I have added an issue to allow new sample types on the fly. See https://www.labkey.org/issues/home/Developer/issues/details.view?issueId=4490
I have heard this request before, though I can't quite remember where. I think that we would want to divide the sample type into two parts -- primary type (blood) and derived type (PBMC, serum, lysed whole blood). Does that make sense to you? Hopefully I'll be able to get to this for 2.3, but can't promise.

2) The Protocol Designer you are using does not have a way to import timepoints in bulk (you have to click and add them). But there are a couple of things you should know in this area:

  2a) Studies can be created without going through the protocol designer (you can just create a study folder directly). Once a study folder is created it is (currently) only loosely associated with the protocol that was used to create it.

  2b) There are indeed new features in 2.3. In particular animal study data is often entered with dates rather than pre-defined "Visits" as in human trials. In 2.3 we will be supporting "Date-based" studies where each animal has a "Start Date" and the visit timepoint is calculated from the Date of the assay or other event. "Visits" are automatically generated based on dates.

  2c) If you import data into a study referencing "unknown" visits, the visits will be added automatically. This works for either the new "Date Based" studies or the existing "Visit Based" ones.

  2d) Within the current study folders (no matter how they are created) there is a way to import a "Visit Map" with visits. This is somewhat tricky but is described here: https://www.labkey.org/Wiki/home/Documentation/page.view?name=visits

Hope the above was helpful. It's very useful to have customers who can help us figure out what the right functionality is.

- Mark