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Progeny Community » Forum: Progeny LIMS - Recent Posts http://www.progenygenetics.com/community/ Progeny Community » Forum: Progeny LIMS - Recent Posts en Sun, 05 Feb 2012 16:53:58 +0000 Conrad Brammer on "Date and time of reaction" http://www.progenygenetics.com/community/topic/220#post-663 Thu, 12 Jan 2012 11:37:38 +0000 Conrad Brammer 663@http://www.progenygenetics.com/community/ Hello Guy, We have a trigger for you to record this information during a reaction. I will email you directly to arrange a desktop session. Thanks Conrad Brammer on "Date and time of reaction" http://www.progenygenetics.com/community/topic/220#post-648 Mon, 12 Dec 2011 12:22:28 +0000 Conrad Brammer 648@http://www.progenygenetics.com/community/ Hello Guy, I will need to run this by one of our developers to see if we can do this with a computed field. It would likely need to be based off a specific reaction, so you would want to make sure this reaction is unique to that particular action (if the reaction were to be included in another action for instance this wouldn't work). I'll go ahead and get this submitted now and let you know the moment this has been addressed. We may need to gather additional info such as the reaction ID of the action you want to use for the trigger, which you can access via Sybase Central. Issue Tracking ID = C1539 I'll let you know when I hear back. Thanks guyygarty on "Date and time of reaction" http://www.progenygenetics.com/community/topic/220#post-644 Mon, 05 Dec 2011 16:30:14 +0000 guyygarty 644@http://www.progenygenetics.com/community/ I would like to add a calculated field to a sample, that shows the time/date 44h after a reaction is executed (or after a workflow stage is executed). Is there any way to access the info in the sample Audit? If not, is there a way to route the current date and time into a static field? guy Conrad Brammer on "change workflow stage for multiple aliquots" http://www.progenygenetics.com/community/topic/178#post-584 Mon, 07 Nov 2011 11:57:05 +0000 Conrad Brammer 584@http://www.progenygenetics.com/community/ Hi Severine, Are you familiar with how to run batch actions? When you create or edit an action, there is an option under "Settings" to allow that action to be run on "Multiple Samples". If you check this box for the action associated with your workflow stage you will be able to move your batch of samples together to the "Next Stage". The trick here is selecting your batch of samples. There are a number of ways to do that. Via stages in the Workflows tab (available in the Windows client): 1. Browse to the Workflows navigation tab. 2. Select the stage your aliquots are currently in (your samples will display below). 3. Highlight your samples, right click and select "Next Stage" Via search criteria from the main screen: 1. Enter search criteria that identifies your batch of samples on the main screen (i.e. Workflow Stage, Sample Type, Extraction Date, etc.) 2. Highlight your batch of samples, right click and select "Next Stage" Via scanned barcodes: 1. Run a sample spreadsheet with the field "Barcode" as your only field 2. Filter the column or include in the query "Barcode" with the "in" operator 3. In the edit box, scan your samples one by one, separated by a comma (no spaces). 4. Run the spreadsheet (this will find all sample barcodes in your list of scanned barcodes). 5. Highlight the list of barcodes by dragging over the list, right click and select "Next Stage" If this is at all unclear, or you would like a demonstration of this, give us a call or shoot us an email and we can set up a GoToMeeting to show you how to do that. Thanks for the post! Severine on "change workflow stage for multiple aliquots" http://www.progenygenetics.com/community/topic/178#post-582 Thu, 03 Nov 2011 16:09:15 +0000 Severine 582@http://www.progenygenetics.com/community/ Hi, What is the faster way to assign the next workflow stage to a multiple of aliquots? Currently, I scan the aliquot barcode, right clic to current stage to move the aliquot to the next stage and I do this for each aliquots. Is it possible to create an action for that? Thanks Conrad Brammer on "Barcode Scanner" http://www.progenygenetics.com/community/topic/132#post-402 Wed, 13 Apr 2011 17:07:49 +0000 Conrad Brammer 402@http://www.progenygenetics.com/community/ Progeny will integrate with any barcode scanner on the market. The scanners themselves simply translate the barcode into a readable text format, so it doesn't really matter to our software where that text is generated. When setting up your LIMS, the first thing you want to do is to take into account the tubes you will be barcoding, how cold your freezers are and finding a label that is appropriate for the size of the tube and can withstand the temperature of your freezers. Then, you want to find a printer that can print to those labels with enough precision to make those barcodes readable. Your last step should be to find a barcode scanner that is capable of reading the barcodes you are printing. Some barcode scanners are more precise than others, so it is best to have those other factors in place. Regardless of what barcode scanner you choose, the scanner will work with Progeny. Thanks for the post! I hope this helps. cinrillo on "Barcode Scanner" http://www.progenygenetics.com/community/topic/132#post-400 Wed, 13 Apr 2011 14:52:50 +0000 cinrillo 400@http://www.progenygenetics.com/community/ Hi we recently purchased the LIMS component, which barcode scanner do you recommend? We will be generating both 1D and 2D barcodes. Thank-you swfouchier on "Samples can't be in multiple plates in Progeny 8?" http://www.progenygenetics.com/community/topic/118#post-391 Tue, 12 Apr 2011 13:54:26 +0000 swfouchier 391@http://www.progenygenetics.com/community/ Apparantly in P8 you can add-save and move-save samples via PED in a exsisting plate/container. Only deleting is not possible. Have not figure out the Import Module yet, but it sound more complicated as it would be via PED. Especially since our Genetic Field Worker are 65+ woman I hope I can keep it as simpel as possible for them. So let's hope the C1255 request is coming through :-). Conrad Brammer on "Samples can't be in multiple plates in Progeny 8?" http://www.progenygenetics.com/community/topic/118#post-382 Mon, 11 Apr 2011 18:07:53 +0000 Conrad Brammer 382@http://www.progenygenetics.com/community/ In regard to the sample viewer from within the Pedigree, this feature was designed as essentially a "read-only" viewer. You can open sample data sheets and view plates, but you cannot add or remove any samples from this window. I have added this as a request, however, and logged it into our database with the tracking ID of C1255. You can track progress of this issue by providing that ID with any member of our support staff. Thank you for your post. Conrad Conrad Brammer on "Samples can't be in multiple plates in Progeny 8?" http://www.progenygenetics.com/community/topic/118#post-381 Mon, 11 Apr 2011 18:01:01 +0000 Conrad Brammer 381@http://www.progenygenetics.com/community/ Hello Sigrid, The only feature you mentioned that is not available to you now in Progeny Clinical is the batch sample creation via right click menu, "to add a sample and immediately also determine how many of the same aliquots I want to add." The end goal, however, of creating these aliquots, assigning them to parent samples and individuals and adding them to plates and positions is available to you now in Progeny Clinical via the Import Module. The Import Module is not a feature exclusive to Lab or LIMS. It is available for all products. If you would like to learn more about the Import Module and how it can be used specifically to address your needs, feel free to give us a call or shoot us an email to set up an interactive desktop meeting to show you how. Thanks, Conrad swfouchier on "Samples can't be in multiple plates in Progeny 8?" http://www.progenygenetics.com/community/topic/118#post-371 Fri, 08 Apr 2011 04:01:29 +0000 swfouchier 371@http://www.progenygenetics.com/community/ An other thing I want to address. If I am in a PED, click samples, view the plate/container I can not delete samples. Why is this? I can add en move, these actions are saved, but deleting is not? Thanks, Sigrid swfouchier on "Samples can't be in multiple plates in Progeny 8?" http://www.progenygenetics.com/community/topic/118#post-370 Fri, 08 Apr 2011 03:50:21 +0000 swfouchier 370@http://www.progenygenetics.com/community/ Dear Conrad, As I posted earlier, we do not have lims. Our Genetic Field workers (GFW) and technicians are the Clinical users and me and one other post-doc are Lab users. No LIMS, no web. The problem in our lab is that the GFW, who visits the patient at home, comes to the lab to add PED info in Progeny and process the blood sample including storage of plasma samples. Since Clinical users do not have full access to the sample options, they put this info in fields I created for this purpose, but they do not have acces to the plate info and therefore they have an excell DB to see where the next sample should go. Of course it would be much nicer if they are able to do this directly in Progeny. Since we only store 3 plasma samples per patient we do not really need LIMS. They also do not need the LAB version. These versions are all well to sophisticated for the actions we want the GFW to perform. And I guess the import module is also not avaliable in Clinical?! I do believe they have the Sample bottum when they open a PED en therfore they could add samples and put them on a plate/container if the plate/container exsists. This would perfect for us, but in P8 they can not add aliquots via this route and therefore it would be most usefull for us that this would be possible when you add a sample plus aliquotes at an individual when you are in the PED. Stephen Miller mentiones once that the differences between Clincial and Lab would change in the future. Is this indeed the case and what would happen then with the sample options? Off course the option will be to expand our current Progeny setup, but this will probably costs us a lot of euros, just to have the ability to add aliquotes by the GFWs/ Clinical users. What do you think about this? Best, Sigrid Conrad Brammer on "Samples can't be in multiple plates in Progeny 8?" http://www.progenygenetics.com/community/topic/118#post-363 Thu, 07 Apr 2011 15:22:57 +0000 Conrad Brammer 363@http://www.progenygenetics.com/community/ >Even if you want to put the same sample in the same plates it wants aliquotes. This means now that I have to add each aliquote one by one. The conversion process will create the aliquots for you, so you would not have to create aliquots one by one. They can also be created in batches after you have converted to Progeny 8. You can do this via actions in LIMS or via the Import Module by importing your aliquot samples and specifying a "Parent Sample Name". >Is it possible to add a sample and immediately also determine how many of the same aliquots I want to add? Yes. You can create an action as a right click menu option in Progeny LIMS to create an aliquot and prompt you to enter the number of aliquots you would like to create. >BTW, Is it true that adding aliquotes in Progeny lab is not possible? No. You can add aliquots via the import module. Simply import the aliquots you'd like to add to the database and include a column for "Parent Sample Name" as long as you identify a sample name that exists in the database the aliquots will be added as aliquots of the specified parent sample. You can also include "Container Name" to import your aliquots directly into a container. Thanks! Hope this helps. swfouchier on "Samples can't be in multiple plates in Progeny 8?" http://www.progenygenetics.com/community/topic/118#post-350 Wed, 06 Apr 2011 08:27:29 +0000 swfouchier 350@http://www.progenygenetics.com/community/ BTW, Is it true that adding aliquotes in Progeny lab is not possible? swfouchier on "Samples can't be in multiple plates in Progeny 8?" http://www.progenygenetics.com/community/topic/118#post-349 Wed, 06 Apr 2011 06:06:37 +0000 swfouchier 349@http://www.progenygenetics.com/community/ Even if you want to put the same sample in the same plates it wants aliquotes. This means now that I have to add each aliquote one by one. This increases the change for typing errors. Is it possible to add a sample and immediately also determine how many of the same aliquots I want to add? Thank you, Sigrid Conrad Brammer on "Samples can't be in multiple plates in Progeny 8?" http://www.progenygenetics.com/community/topic/118#post-332 Thu, 24 Mar 2011 12:29:09 +0000 Conrad Brammer 332@http://www.progenygenetics.com/community/ Hello Tsvyatko, The database conversion from Progeny 7 to Progeny 8 handles samples on multiple plates by creating an aliquot sample for each "duplicate" sample. The aliquot will be represented as "[Parent Sample Name]_[auto increment]". In other words, if the sample "DNA326" is on 3 different plates in Progeny 7. The conversion will represent those samples as the following: DNA326 DNA326_1 DNA326_2 They will retain all of the data that was present in Progeny 7, and will continue to be linked to the same individual. The only thing that changes is the Sample Name and Barcode. Thanks for the post, Conrad tdorovski on "Samples can't be in multiple plates in Progeny 8?" http://www.progenygenetics.com/community/topic/118#post-327 Tue, 22 Mar 2011 13:37:21 +0000 tdorovski 327@http://www.progenygenetics.com/community/ Hi Dave, I was wondering, how do you guys handle these when upgrading and existing Progeny7 database to 8, where there are already samples into multiple plates? Please let me know Regards Tsvyatko nboutaoui on "Intermec PX4i vs Zebra TLP2844 for barcode printing" http://www.progenygenetics.com/community/topic/100#post-326 Tue, 22 Mar 2011 11:42:12 +0000 nboutaoui 326@http://www.progenygenetics.com/community/ Hi All, Thanks a lot for your very helpful feedback. Nadia David DeRam on "Samples can't be in multiple plates in Progeny 8?" http://www.progenygenetics.com/community/topic/118#post-319 Wed, 16 Mar 2011 21:40:25 +0000 David DeRam 319@http://www.progenygenetics.com/community/ Jesse, There are several reasons why you may not want to add a sample to more than one plate. There were best practice considerations in making this change in version 8. You are correct that adding as aliquots is the right approach. This is a longer conversation than we may want to have in this context. My understanding is that you have been in touch with Conrad and you are planning to discuss. mccanejd on "Samples can't be in multiple plates in Progeny 8?" http://www.progenygenetics.com/community/topic/118#post-318 Wed, 16 Mar 2011 14:17:49 +0000 mccanejd 318@http://www.progenygenetics.com/community/ I've been thinking about this, and I suppose one solution would be to create an aliquot of the sample if we need to run it on another plate. I'll play around with this for a while and see how it works. mccanejd on "Samples can't be in multiple plates in Progeny 8?" http://www.progenygenetics.com/community/topic/118#post-315 Tue, 15 Mar 2011 15:48:12 +0000 mccanejd 315@http://www.progenygenetics.com/community/ While setting up our new database, I noticed a few things that I could do in Progeny 7 but could not do in Progeny 8. One main difference I noticed is that I cannot add a sample to more than one plate (probably due to a plate being treated as a container rather than a plate, as it was in Progeny 7). When I add a sample that is already part of one plate to a new one, the sample is removed from the original plate. Because of this, I can't have a sample located in a container as well multiple plates. This functionality was essential to our inventory system. Is there any way to have this feature in Progeny 8? Or is it something that may be returned to the program in the near future? Thanks, -Jesse Conrad Brammer on "unassign sample from individual" http://www.progenygenetics.com/community/topic/109#post-293 Tue, 15 Feb 2011 18:23:53 +0000 Conrad Brammer 293@http://www.progenygenetics.com/community/ That makes a lot of sense. Thanks for taking the time to put that into context. I can see why it would be beneficial to unassign samples, especially as part of an "exhaust sample" action. I'll update that request with this information. That will help to push that into development :) jamie-lheureux on "unassign sample from individual" http://www.progenygenetics.com/community/topic/109#post-291 Tue, 15 Feb 2011 17:40:34 +0000 jamie-lheureux 291@http://www.progenygenetics.com/community/ The reason we want to unattach samples from individuals is that we sometimes run out of, discard, or no longer have a sample for a specific individual for a variety of reasons. We want to keep a record of the sample for tracking purposes, but we want the database to accurately reflect that we no longer have a sample for that person. The biggest reason for this is that we utilize the sample count system field on the individual to see whether a person in a family has a sample. We then use summary fields to characterize each family into trios (where we have samples from the child, mother, and father), diads (samples from child and one parent), etc, etc, so that we can easily select families for specific types of studies. The best way we could figure to have this be accurate when a sample no longer exists would be to unattach the sample from the individual. However, another way to meet our needs would be to have summary fields much like the ones that are available now that count how many individuals in a pedigree meet some individual level criteria, but instead to have them count how many samples attached to one person meet some sample level criteria. Then we could query for individuals who have at least one blood sample versus one buccal swab sample etc. I'd be happy to talk more about this if needed. For now, I think #2 will work - I think I tried #1 before posting this and it said it couldn't find an individual named "". But, I still think a reaction to allow you to unattach a sample would be useful in the long run. Conrad Brammer on "unassign sample from individual" http://www.progenygenetics.com/community/topic/109#post-284 Mon, 14 Feb 2011 18:00:16 +0000 Conrad Brammer 284@http://www.progenygenetics.com/community/ Hi Jamie, I can put this in as a request. Can you help me understand why you are needing to unassign you samples? The better we understand the need, the better we will be able to design a new feature for that. In the mean time, there are definitely easier ways to work around this. 1. You could run a SS of all the samples you want to "unassign", export that list of samples, and then reimport those samples using the Import Module. When you reimport, include a blank column and specify that as the Unique ID for assigning individuals to the samples. This will update the individual names to a blank value, and in effect, "unassign" the samples. 2. OR you could just create a fake individual, assign all the samples to that individual and then delete the individual. jamie-lheureux on "unassign sample from individual" http://www.progenygenetics.com/community/topic/109#post-281 Wed, 09 Feb 2011 19:39:28 +0000 jamie-lheureux 281@http://www.progenygenetics.com/community/ Is there an easy way to unassign a group of samples from individuals? The only way I can think of to do it is to right click on each sample and select edit sample and then uncheck the box that says "assign this sample to an individual". I was wondering if it would be possible to have this added to the reactions that are pre-defined, like assign to individual or remove from container. Then, we could just do an action to all of the samples we want to unassign from individuals. jamie-lheureux on "Intermec PX4i vs Zebra TLP2844 for barcode printing" http://www.progenygenetics.com/community/topic/100#post-280 Thu, 03 Feb 2011 19:15:16 +0000 jamie-lheureux 280@http://www.progenygenetics.com/community/ In addition to the TLP 2844, we also use the Zebra S4M. It is more expensive, but it is networkable and allows us to print on self-laminating labels that are partially clear so you can see the volume in the tube even when the label wraps all the way around the tube. We use the TLP2844 at our collection sites for labeling the initial tubes of blood etc, and the S4M in the lab for the DNA tubes. Conrad Brammer on "Intermec PX4i vs Zebra TLP2844 for barcode printing" http://www.progenygenetics.com/community/topic/100#post-279 Thu, 03 Feb 2011 10:52:55 +0000 Conrad Brammer 279@http://www.progenygenetics.com/community/ Hello Nadia, Severine just brought this to our attention and it seems that production on the TLP 2844 has been pulled. The important thing is that you get a printer that uses the core programming language EPL2. Many labeling printers will have multiple supporting drivers you can install, so you just want to be sure that you install the EPL driver. Happy to hear the GX430T is working well for you, Severine. Thank you for passing along that recommendation. Conrad Severine on "Intermec PX4i vs Zebra TLP2844 for barcode printing" http://www.progenygenetics.com/community/topic/100#post-277 Wed, 02 Feb 2011 11:06:15 +0000 Severine 277@http://www.progenygenetics.com/community/ Hi Nadia, We are using the Zebra GX430T (300DPI) and it works really well. It seems like the TLP 2844 is not on the market anymore. Severine Conrad Brammer on "Intermec PX4i vs Zebra TLP2844 for barcode printing" http://www.progenygenetics.com/community/topic/100#post-258 Tue, 18 Jan 2011 15:13:31 +0000 Conrad Brammer 258@http://www.progenygenetics.com/community/ Hi Nadia, I would recommend the Zebra TLP 2844, as this is the printer we have here on site. This makes troubleshooting any issues you may have much easier for our support team. Features/Specifications for the Zebra TLP 2844: Maximum label and liner width: 4.25-inches Minimum label and liner width: 1-inch Resolution: 203 dpi (8 dots/mm) Print Speed: 4-inches/sec Full list of specifications: Print methods: Direct thermal/thermal transfer (TLP) OpenACCESS design Head-up sensor Resolution: 203 dpi (8 dots/mm) Memory: Standard: 256 KB SRAM; 512 KB Flash Print Width: 4.09-inches maximum Print Length: 11-inches Print Speed: 4-inches/sec Media Sensors: Reflective, Transmissive Maximum label and liner width: 4.25-inches Minimum label and liner width: 1-inch Maximum label and liner length: 11-inches Maximum roll diameter: 5-inches Core Diameter: 1-inch Media Thickness: 0.003-inches Media Types: black bar, black mark, continuous, continuous receipt, die-cut, fanfold, gap, notch, notch sensing, notched, perforated, receipt, roll-fed, tag, tag stock Ribbon Outside Diameter: 1.34-inches' Ribbon Standard Length: 244 feet Ribbon Ratio: 1:1 media roll to ribbon ratios Ribbon Setup: Ribbon wound ink side out Core Programming Languages: EPL2 Thanks, Conrad nboutaoui on "Intermec PX4i vs Zebra TLP2844 for barcode printing" http://www.progenygenetics.com/community/topic/100#post-255 Tue, 18 Jan 2011 12:11:13 +0000 nboutaoui 255@http://www.progenygenetics.com/community/ Hi, We recently Progeny Suite and would like some feedback about Barcode printers: Intermec PX4i and Zebra TLP 2844 such as Print Width, resolution, print speed, ability to be networked... Your feedback is much appreciated. Nadia B