2015 Import Lesson 2

Runtime
10:24

Transcript

Video Transcript – 00:00

Hi, and welcome to the second installment of our series on Importing Samples and Aliquots into Freezerworks. In the first example, we imported sample records and we create an aliquot based on the number of aliquots for each sample.  In this example, we’ll have a spreadsheet that will have the Freezer Box Location for every aliquot.

Creating the Import File – 00:33

So this is a record of a spreadsheet of aliquots, and here’s what we’re going to be importing.  Here, as you can see, we have 10 sample records, but actually, each one is one aliquot, so this is actually 10 aliquots and each has a Sample ID.  For example, we have three aliquots with the Sample ID 40000 (a1, a2, and a3).  We want to put these into one sample record.  Here again, we have three Sample IDs of 40,001 and each one represents one aliquot so we want to put these three aliquots under another different sample ID. The other four here are all unique Sample IDs, now Freezerworks can do that, it will take the unique identifiers which we will call the sample ID here, and attach aliquots as needed.  So, let’s go ahead and show you how to do that.

Saving the Text File – 01:46

So first, what I want to do again is to save this Excel™ spreadsheet as a .txt or a text file of some sort. Last time we did .txt Tab delimited; let’s go with Comma delimited this time.  Let’s save it as a Comma delimited file, and these warnings are okay, we just hit yes everything’s good, and now what I want to do next is find the freezer that I’m going to put this box into.  

Finding empty freezer locations using Explore Freezers – 02:20

I’m going to go to Explore Freezers and I have a freezer over here called Demo Physical.  Demo Physical has two freezer sections here, Top Shelf and Shelves 2 thru 5.  Top Shelf has a subdivision rack, then the subdivision box, and each box has rows and columns.  So, this is subdivision 1, then subdivision 2, then 3, and then 4.  We are importing rows and columns, so we’re going to import positions 3 and 4 into our freezer section Top Shelf.  This spreadsheet that we are going to import represents a complete box, so we want to go ahead and import the box into this freezer.  We can see that Box 1 in this rack already has a box in there, Box 4 has a box.  Box 2 and Box 3 don’t show up here, that means that those positions are free in this rack, Rack A.

Creating the Import Format – 03:31

So, let’s go ahead and import.  We’re going to import this box into Box 2 of Rack A, so let’s go ahead and do that.  Let’s go to Sample Management – Import Data and we will create an Import Format for this. We’ll call it Import 2. It has a header record; the first record in the spreadsheet had the header so we select Header Record Included in Import File so Freezerworks doesn’t try to import that first row.  It’s a Comma delimited file.  The Date Format is the same as the first example, so we’re good here.  We don’t have to worry about the Time Format; we are not importing a time field.  Open the file, let’s find it, here it is, .csv Import Samples with vials and locations.  

Mapping Fields – 04:21

Let’s open it and then Freezerworks we’ll try to map based on our file headers.  There is a field in Freezerworks called Sample ID.  I can go ahead and select that, or change it.  I’m going to change it, as we did in the first example, to Sample ID Import, so highlight this and select Sample ID Import and Map. Now Sample ID will go into my Sample ID Import.  Sample Date will go into Sample Date, that’s good, I like that.  Type, it did not find a Type field, so we will go to aliquots, because the type again – BUF, are going to be put into Aliquot Type. So I Map Type into Aliquot Type.  Patient ID goes into patient ID, that’s still good.  Hospital going into Hospital, that’s still good.  I need to know where in the freezer I’m going to put the row and column, and again, as we saw earlier, we’re going to go into positions 3 and 4.  This is the rack and then the box, the row, and the column. Position 3 and Position 4 are row and column.  So Position 3 goes here and Position 4 will go here. 

Import Settings – 05:54

Okay, the mapping is done.  Now I need to go to Import Settings to tell Freezerworks what kind of import this is, and again we are Adding Samples and Aliquots actually to Freezerworks.  Now, how are we going to create the aliquots?  We are going to create them this time using our interactive auto-assign.  That’s where we select the freezer and tell it where to put the samples, so you can see here that we will be prompted during the import for a freezer and a next assignable position (NAP) to which the aliquot will be assigned.  No problem here, let’s go ahead and do that.  We have the unique identifiers, again Sample ID Import, and that’s where the Sample IDs will go.  So, let’s save this format.  

Importing .csv File – 06:50

Let’s go ahead and go back into it now and do the import.  This is the file that we are importing, we need to select our freezer, and again that was the Demo Physical, the freezer section which was our Top Shelf, and we’re going to ignore these grayed out areas (you don’t have to worry about that).  This is our the next assignable position in Freezerworks, but we’re going to go ahead and adjust it, we’re going to go ahead and assign these into Box 2.  So this box is going to be Box 2 in our Top Shelf freezer section starting at Rack A.  So these are grayed out, that’s okay, Freezerworks is going to start at Box 2 and then assign the locations as the spreadsheet has it set up.  We select OK, it writes the import data, and our import is complete.  We have 6 samples created, with 10 aliquots all together in those 6 samples.  

Viewing Imported Data – 08:05

Let’s go ahead and take a look at them.  We’ll go ahead and view them by sample, and here are our six sample records that we’ve imported.  I have a special list format that I want to use in this situation, called Importing, that will help us look at this a little bit better.  We can see here that our first record, Sample ID Import 4000, has 3 aliquots in there, 4,0001 has 3 aliquots, and those other four samples are 1:1 (One aliquot to one sample).  Let’s go ahead and take a look at these records as they got imported.  Double-click on the first one and we can see here, (I have a special form I want to use for this import, let’s use it), that here is Sample ID 40,000, the first one.  Here is a Patient ID,  In the hospital that were imported at.  As you can see, we do have three aliquots stored, and here they are imported as we wanted them to be a1, a2, and a3.  Okay, if we then go ahead and go to the next record, to 40,001, we can see 1, 2, and 3 again.  Everything looks good.  Then we go to the next record, which was 40,006, we can see it’s a 1:1 relationship, and so forth (so the next one will be a 1:1).  As you can see here, you go through that we can see that all these samples were imported.  So I was able to import that whole box into that freezer.  Now, if I want to look at the aliquots I can come here and look at these as well from this respect.  Let’s go ahead and take a look at our import using Explore Freezers.  Let’s go ahead and go into Demo Physical, let’s go to the Top Shelf – Rack A, and here is box 2.  It’s no longer blank, we have a box, Box 2.  Here they are, the samples that we just imported, the BUFs. 

Conclusion – 10:10

That is how you would import a box using interactive auto-assign, importing, and Freezerworks, thank you.

Next Video – 2015 Import Lesson 3