Batch Entry in Freezerworks Unlimited

Batch Entry Introduction – 00:00

Hello, and welcome to our class on how to use Batch Entry in Freezerworks Unlimited.  In this lesson, we will learn how to create new records using Batch Entry.  Now, your lab may have samples coming in regularly for processing and storage.  Using Batch Entry, you can quickly create records while improving the data integrity by automating the data entry process.  Batch Entry can be used to accomplish the following: you can create new records by scanning pre-existing barcodes, you can create new records by auto-assigning and auto-generating ID numbers, and you can create aliquots and aliquot data for those samples (including the freezer locations).

Setting up the Batch Entry example – 00:50

We're going to start with an example in which we have a protocol where 15 samples are coming into the lab for processing.  For each of these samples, we're going to create the sample records and three cryovial aliquots (one serum, plasma, and DNA).  We're going to create these records ahead of time so that we can print and have labels ready for processing and freezing, and we're going to pre-assign the vial locations.  Let's go ahead and get started.

Configure Batch Entry – 01:25

Okay, so to create a Batch Entry we need to first create a Batch Entry format, and to do that we go to System Admin – Configure Batch Entry.  Here we create a new format.  We select Add New and we'll give this format a name.  We'll call it Protocol 2500. We can give a description if we’d like.  After the name and description, we tell the format how we want it to create samples.  Are we going to create sample records by scanning or typing in a key field?  Or are we going to auto-generate a number, or maybe, import a file?  We'll show each of these options.  

Scanning Key Field Format Configuration – 02:20

The first option we're going to do in this example is we're going to scan a key field.  Because we have 15 samples and the information is barcoded, we're going to scan those fields in, and then create the records that way.  So, with Scanning Key Field selected, we select the barcode that field that we're scanning refers to.  This situation refers to our Patient ID.  

Adding Sample Fields to Batch Entry Format – 02:50

The next thing we want to do is determine for every sample that we scan in, what are the fields that we want entered and what will Default Values be for each of these.  So, these are the sample fields, and we determine the sample fields that we're going to enter in the batch process and what the values will be.  After that, we'll go to the aliquots and determine if there are any aliquots that we're assigning and what those fields will be.  So, we select Add New.  We're going to add new fields to this process, and we select the field and then the values that we want those fields to be.  Now, one of our fields here will be the Protocol, and we want the Protocol to be 2500. So, I select the field and the value, Protocol – 2500. I hit save and then the screen clears out again and we put the next one in.  We want to put a Sample Date in, so let's select a sample date (select the field Sample Date).  Here, we can put a default date which could be the current date or we can leave this blank or we can say yesterday's date, tomorrow's date, whatever the format may be.  Now, in a situation like this, maybe we don't know until we create the records what the sample date will be.  We can leave this blank and fill this in when we actually create the fields; right now we're just creating the format.  Let's leave this blank right here for now, and then let's hit Done here.  It’ll show that we have two fields so far.  We'll scan in the Patient ID and when we create the records it’ll put a Protocol 2500.  The sample date we'll assign at the time that we create the Batch Records.  The next field will be the Hospital, so let's scroll to the hospital field and in our Hospital value let's add a new one here.  Let's go ahead and put in Providence.  The last field will be our Study Visit.  Let's go to the Study Visit and enter our value as Baseline.  Save that.  When we’re done entering we hit done, and here are our sample fields and the values that they will have.  

Adding Aliquot Fields to Batch Entry Format – 05:35

Now, for each sample record that we are going to create, we want to create three aliquot records (Plasma, Serum, and DNA).  To do that, we come to the tab Aliquot Fields.  Now, we have two screens here that we can see.  We need to include which aliquot fields we want to enter during this batch process.  Down here we'll assign number of aliquots for each and if we want to put them in a freezer at this point during our batch process.  Let's first decide which aliquot fields we want to include in this batch process.  We're going to include three of them, Aliquot Type, Initial Amount, and Current Amount.  So, let's go to Add New and then we select Aliquot Type, we'll also add Initial Amount, and then the Current Amount.  We can add as many fields that we want to include here, as well.  As you can see, as we enter these they get entered over here on the Configure Aliquots.  There are only three fields that we want to enter during our batch process that are aliquot fields, these three.  Now, we need to determine how many aliquot we're going to create, what type, and what freezer they’ll going into.  We come down to Configure Aliquots.  Let's start here by selecting Add New.  What we want to do is we want to create an Aliquot Type of Plasma.  Let's go ahead and start with Plasma.  We're going to create one aliquot of Plasma, and let's decide, do we want to configure the Batch Entry to select the freezer to put it in?  Let's go ahead and do it.  Let's put these into the DEMO freezer, and we're going to have an initial and current amount of two.  So during our process, we will create one Plasma aliquot, we'll put it in the freezer DEMO, and it'll have an initial and a current amount of two.  Let's save that. Now, screen is clear again for a next entry.  Let's hit cancel right here, just to show you what we have.  We have one aliquot, DEMO freezer, Plasma.  Let's now add our Serum aliquot.  Add New and let's select a freezer that that would go into.  Let's go ahead and put these serums into Freezer 1.  Freezer 1 is our serum freezer, one aliquot of serum will go into Freezer 1, and let's go ahead and make the defaults two again.  As you can, see I've created green for my serum aliquot types.  Let's save that.  Then for our last one, we're going to store one aliquot of DNA.  We don't know which freezer we're going to put it into.  We may know the freezer, but we don't want to assign freezer locations for the DNA aliquot, so we're going to do that at a later time.  So for DNA, let’s leave Select a Freezer blank, and for the amounts (we're counting cells), let's go 500 here.  Okay, and then we're done.  We have our three aliquots.  Hit cancel here.  We see for every sample we're going to create an aliquot of Plasma, an aliquot of Serum, and an aliquot of DNA.  Now, at any time, if you want to modify any of these we can go ahead and go into those, we can highlight it, and select Modify and make any changes we need to make to this format.  The other thing that we can do is we can delete.  If we decide now we don't want to store DNA, we can delete it, or if you want to remove fields.  Lastly, we can assign these formats to groups.  We can say certain groups can use this data entry format. For this format, say that Group 1 is the only group that is allowed to use this format.  If you are not a member of Group 1, then this format will not be available to you.  Okay, we're done here.  Let's go ahead now and save this format.  

Saving a Backup Prior to Batch Entry – 10:35

Now, let's create some samples with it.  Select save.  I come to a blank record here and let's cancel out.  We can see now that we do have one format in Configure Batch Entry, Protocol 2500.  Let's go ahead and close this.  Now, let's test it by going to Sample Management - Batch Enter Samples.  First, you’ll come to a warning prompt here letting you know that batch processes do not have a rollback function.  So, it’s a good idea to make sure you have a backup of your data before you do a batch process, particularly a large batch process.  If you want to revert back to what you had before, you can just go back to your back up.  In these situations, if you do a batch process and you don't like what you did (it didn't work the way you wanted it to) and you want to delete and start over again, you can go ahead and delete those samples and aliquots.  However, we suggest that when batch processing, it’s always a good idea to have a backup.  

Selecting a Batch Entry Format – 11:44

Let's select OK here.  We'll come to this window and a list of all the available Batch Entry Formats available to you will be listed here.  There's only one, Protocol 2500.  Fortunately, I'm a member of the group, Group 1, so this is displayed.  I will go ahead and select it now.  As you can see here, Protocol is 2500, Sample Date was defaulted to the current date (if I want to change it I can do that as well), Hospital is Providence, and Study Visit is Baseline.  I can see here that we have our aliquots: Plasma, Serum, and DNA.  The freezers that are assigned too, if there's a freezer assigned to it.  And the Starting Position.  Now, this is the Next Assignable Position in this freezer.  This is where you stopped before you last stopped entering samples.  So, D 1 in Box 2 of Rack A is where the Next Available Position is in this freezer. I can continue to assign these samples starting here, or perhaps I want to start a brand new box.  I can go ahead and change this at this point.  Let's say that we want to move ahead and we want to enter these samples into Rack A – Box 3 of our DEMO freezer.  These can be changed here during the assignment process, to prepare it.  We have our defaults set and we can make changes as we need to.  Let's say, that and so we've got that, like that.  Let's go to Serum now.  In serum, last time I was entering samples I stopped at Box 2 – 3 – F, so now I'm at 3 – G.  I can continue to go forward from there, or if I want I can move the Next Available Position to a different location in the freezer.  Let's go ahead and do the same thing.  Let's start at Box 3, and we'll start at 1 – A for our Serum samples.  Save that.  And then the DNA, we’ll leave blank.  We're going to assign a freezer location to that at a later time.  

Creating a “Scanning Key Fields” Batch Entry Format – 14:05

Now, since our format was set as one that has us scan or enter the ID numbers to create the records, we will have 4 tabs to enter up to 200 ID numbers to patient ID (that was the field we chose during our formatting) and is how we were going to assign these samples.  We can do up to 200 at a time.  Now, I have got here a list of barcodes. I've got 14 of them in order and I was just going to enter these in.  Now, I have these barcodes so I can just scan them and I will do that.  I could also enter these by the keyboard, so it's really nice if you have a barcode (if these are barcoded vials maybe or barcoded reports).  Let me go ahead and start that, and I'm just going to go down the list here and scan these barcodes.  As you can see, they're all in order.  I can skip around too if I’d like.  Just scan all these. So, I have got 14 patient numbers that I've scanned in, that I'm going to create records for.  So, here are the 14, and I'm going to create 14 of these with this data in my sample fields and this data in my aliquot fields.  Let's go ahead and create the samples now.  Okay, I'm about to create 14 samples each, with 3 aliquots. Do you wish to continue?  Yes, that's exactly what I want to do, so I have 14 samples here not 15 like I thought earlier. 

Completing the Batch Entry – 15:50

Let's go ahead and hit Yes.  Now the samples are being created.  Then the next window that will appear will be the Label Printing window here.  If I wanted to print labels at this point for these samples, I can go ahead and select the format and such and print labels for these samples that I am creating.  Let's go ahead and cancel, I'm not going to print labels right now.  Hit Cancel if I'm not going to print labels, and then we see the samples.  Here are our 14 new samples.  And as you can see, they're here in the order that we scanned them into that template.  We've got a Sample Date, an Internal Barcode was assigned, and we have three aliquots for each or these sample records.  Two of those with positions, remember, the DNA samples do not have positions yet, so that shows up as 2.  Here's our Patient ID and here's the Protocol field.  Over here will be the Hospital field, and the Baseline as our Study Visit.  Now, notice that this field here, Sample ID, is blank.  Let me double-click and go into one.  What that is, is that is a Sample ID that is assigned when you enter a sample.  So when I go in here and it’s blank, the code says “Yeah when you go into a sample record, if there's no sample ID assign one”, so it's assigned this one here.  We can see here that our data is here.  We have our three aliquots and so forth.  If I go to the next record, record 2, again we have our records and so forth.  As I go forward, each time I go to the new record, Sample ID is filled in automatically.  So, if I save and close this, you can see the four I went into have sample IDs assigned.  If I want to assign these at the time of Batch Entry then I need to include Sample ID as one of the fields that I use in my template.  Since I didn't, I wanted to get these assigned I'd have to go and select every one of them.  Let's go ahead and do that by just simply scrolling through all of these.  As you'll see, as I do this, the numbers get assigned. Now they're all assigned.  So, I've got my 14 records quick and easy.  Yes, for the most part, it was pretty painless.  

Creating a “Using Auto-Generating Numbers” Batch Entry Format – 18:44

In this example, we're going to go ahead and go back to our Batch Entry template. Now we're going to create those samples again, only this time we're going to show you how to do it using a Freezerworks auto-generated ID number instead of scanning in Patient IDs.  So let's go back to System Admin – Configure Batch Entry.  Let's make some modifications to our previous format by selecting it and making a duplicate of everything.  So I've selected Protocol 2500, hit Duplicate, and now I have a duplicate of that.  Let's go into it.  In this situation, what we're going to do to do is, rather than scan in the key identifier; we're going to let Freezerworks assign the key identifier by using auto-generating numbers. Freezerworks has identified three fields available for the sample records that are auto-generating numbers.  Internal Barcode ID, which Freezerworks assigns to every sample it's created.  As well as the Globally Unique Sample ID, these are system maintained files by Freezerworks.  Sample ID is another auto-generated number that we created as a User Defined Field.  Let's go ahead and use that one, that's the one we saw earlier, when we were working with the previous Batch Entry.  Where we double-clicked and went in and assigned those auto-generated Sample IDs.  In this situation, we're going to select that as the field to auto-generate our records by so it won't be necessary to go in and assign them after we create the records. They’ll be assigned as we create the records.  Let's go ahead and change the Hospital here, let's change it to this.  Then, let's go to Study Visit and let's make the default value for Study Visit, Pre-entry.  As long as we're here, let's go ahead and change the DNA and put it in a freezer.  So with the DNA samples, let's go ahead and put them into a freezer.  Let's assign two Serums for every sample and let's assign three Plasmas for every sample. So, in this situation we're going to create 6 aliquots for every sample we create, three Plasmas, two Serums, and one DNA.  

Batch Entering Samples with “Using Auto-Generating Numbers” our new Format – 21:30

Let’s save this format and let's Batch Enter our samples using this new format.  Sample Management – Batch Enter Samples.  Let's select this new format.  Here we just put in the number 15; we don't scan the numbers in because Freezerworks is going to auto-assign them.  We've got our data here.  Sample Date is defaulted to today's date.  Let's go ahead and leave it like that.  We've got our three aliquots.  Plasma, we're going to start here at B – 5, right where we stopped before the last time we did this.  We stopped at B – 4, so B – 5 is the next one.  As well as for the Serum, we stopped at 2 – E and now we’re a 2 – F.  Our Next Assignable Position for the DNAs are going the Cryo Tank, this is our Next Assignable Position.  We'll just keep going from this point here.  So that looks good, let's go ahead and create our samples.  So we are about to create 15 samples with six aliquots, and that's exactly what we want to do. Let's say Yes and let the processing take place.  Again, we can print labels at this point, let's keep going. Here are our 15 samples.  As you can see, in this situation, Sample ID is assigned and we have our 6 aliquots for each sample record.  All of them have positions.  Double-click into a record, we can see that we've got our three Plasma aliquots, our two Serum aliquots, and our one DNA aliquot into the freezers that we assigned them to.  So, we've got location assigned, we have samples created, and aliquots created.  Let's go ahead and close this, and that is another example of how we can batch enter.

Creating an “Import File” Batch Entry – 23:35

The third example that we want to give you is using an import file.  In this situation, we'll go back to Configure – Batch Entry.  Now, let's go back to the Protocol 2500 that we created.  In this situation, we're going to create sample records by Import File.  The import file is going to have a list of Patient IDs, so we're going to import the Patient ID, and here it is.  Let's go ahead and take a look at that import file.  I'm going to open it up in Excel.  It's just a one record field as we can see here, one field per record.  So, let's go ahead and take a look at that.  Here it is, we've got a list of ID numbers here.  These are Patient IDs.  As you can see here, we do not have a header field.  If you've got a list of numbers that you want to create samples by, you would go ahead and put them in a text file.  You can read them in Excel, but make sure that if you do, you want to save it as a .txt tab delimited format.  Don't save it as .xls, Freezerworks can't read the Excel format.  It needs to read the standard ASCII text format, which is down here.  So, we've already done that, so let's go ahead and import these numbers and create samples for these.  So, Import File, we'll leave this setup the way it is, and let's go ahead and hit Save.

Batch Entering Samples with “Import File” our new Format – 25:42

Now we will batch enter those samples.  We come and select that format and down here we see Import IDs.  Let's go ahead and import the IDs by selecting that.  This is the file we want to import.  10 numbers are imported correctly, so they're imported.  Now, the next step is to create those samples based on those numbers.  Let's create ten samples, each with three aliquots.  Again, we're not going to print labels at this point and here are our ten samples each with three aliquots.  These are the Patient IDs that we imported.  In fact, let's go ahead and take a look at that.  See here that we've got our ten sample Patient IDs.   They were imported and a set of records were created.  Double-click and we go in and look at our import.  

Things to Remember – 27:05

So in conclusion, let's remember some things about Batch Entry, (things to keep in mind).  Whenever we batch enter samples with User Defined Fields that they have default rules, these rules will not take effect under Batch Entry, so include these in your Batch Entry format.  When you're creating a Batch Entry format, and you've got fields that usually you have entered that our default, these won't be created unless you include them in your Batch Entry format, and then place the default entry in your format as well.  Also, again we saw this earlier, if you have a User Defined Field as an auto-generated number, it will not be created in the Batch Entry format unless you include that as a key identifier, as we did in the second example.  We created the Sample ID, made the Sample ID the key identifier, and then they were created during Batch Entry, whereas, if we didn't include that then we had to go into each record individually to auto-assign auto-generate those numbers.  Also, just remember that we don't have to enter aliquot data during Batch Entry.  We can just create sample records and leave the aliquot field information tab screen blank.  If we do something like that, we could always create aliquot records at a later time.

Conclusion – 28:40

I think this concludes our class on Batch Entry and thank you very much for attending. Bye Bye.