http://www.progenygenetics.com/community/ Progeny Community » Forum: Progeny Clinical - Recent Posts en Sun, 05 Feb 2012 16:55:13 +0000 http://www.progenygenetics.com/community/topic/238#post-681 Fri, 03 Feb 2012 17:43:10 +0000 freeseek 681@http://www.progenygenetics.com/community/ <p>I want to import a table we have with information about samples. Though, the samples don't exist in Progeny, so they are not going to match anything pre-existing in the database. I would like for them being created. Is this possible? Or do I have to create them first one by one and then import the data? </p> http://www.progenygenetics.com/community/topic/214#post-645 Tue, 06 Dec 2011 13:08:31 +0000 Tokhir Dadaev 645@http://www.progenygenetics.com/community/ <p>Right click on the folder with pedigrees that are not UL.<br /> Select "Copy Features to Folder..."<br /> Select your pedigree with UL.<br /> Tick features you want to copy. I think you need to tick "Customize Options".<br /> Then OK. </p> http://www.progenygenetics.com/community/topic/214#post-637 Thu, 01 Dec 2011 23:56:05 +0000 ERamigenics 637@http://www.progenygenetics.com/community/ <p>I know that you can change the proband arrow in the properties of each pedigree, but is there a way to change it to a default UL position for every pedigree in a folder? It's very frustrating to have to change each time I add a pedigree. Thanks! </p> http://www.progenygenetics.com/community/topic/122#post-636 Thu, 01 Dec 2011 23:52:39 +0000 ERamigenics 636@http://www.progenygenetics.com/community/ <p>Totally agree. The arrows were a much quicker and more reliable way to add. Thanks! </p> http://www.progenygenetics.com/community/topic/139#post-552 Fri, 16 Sep 2011 10:20:13 +0000 CJohnson 552@http://www.progenygenetics.com/community/ <p>Can you please tell me where to get the BRCA.exe and rates.dat files that I need in order to use the BRCA risk calculations in Progeny 8?</p> <p>Thank you! </p> http://www.progenygenetics.com/community/topic/168#post-544 Thu, 08 Sep 2011 15:38:41 +0000 Conrad Brammer 544@http://www.progenygenetics.com/community/ <p>Hello Kai, </p> <p>If you mark the "import into tables only" option, the spreadsheet will import your data as rows within a Table field. It will not import data into any flat fields that you may have on the spread sheet. </p> <p>Please note that a Table field should not be confused with a Lookup Table field. A lookup table field works more like a drop down field for an import like this. The only difference is that the associated values are linked to a Lookup Table value, whereas a drop down value is not.</p> <p>Does this help resolve your issue? </p> http://www.progenygenetics.com/community/topic/167#post-543 Thu, 08 Sep 2011 15:30:49 +0000 Conrad Brammer 543@http://www.progenygenetics.com/community/ <p>Hello Kai, </p> <p>It sounds as thought you are importing into the spread sheet. If you want to import using pedigree and UPN, you can do so by identifying that the number of unique identifiers in the import file to be matched with the spread sheet is "2" rather than "1". This will find any row matching both values for Pedigree Name and UPN and will import your data. </p> <p>Does this help? </p> http://www.progenygenetics.com/community/topic/168#post-542 Thu, 08 Sep 2011 12:49:04 +0000 kai 542@http://www.progenygenetics.com/community/ <p>Hello,<br /> I try to import data into table field using the "Global ID" as unique ID<br /> I met a problem when I try to import the data.<br /> after I click import button, I check “import into tables only” box, then click OK.<br /> A window “import cancelled” pop up, say “no tables were found in this spreadsheet, please check your settings.”</p> <p>Do you know how to solve the problem? May I need to setting something before I try to improt data into table field?<br /> Thanks,<br /> Kai </p> http://www.progenygenetics.com/community/topic/167#post-541 Tue, 06 Sep 2011 16:19:47 +0000 kai 541@http://www.progenygenetics.com/community/ <p>Hi Sean,</p> <p>Is there possible to let me know the logical of SQL script behind the import function?</p> <p>Thank you,</p> <p>Kai </p> http://www.progenygenetics.com/community/topic/167#post-540 Fri, 02 Sep 2011 10:03:50 +0000 Sean 540@http://www.progenygenetics.com/community/ <p>Hi Kai,</p> <p>We would have to see the data being imported to give you a complete diagnosis of the data errors, but from what you entered above I can make a few preliminary guesses. Assuming that these are individuals you are importing to the database, you will not want to use the Pedigree Name field as a unique identifier.</p> <p>Unique identifiers can only occur once in a database table. For individuals, the UPN or Individual Name usually serve as this unique value. Try the import again but remove the Pedigree Name as a unique identifier.</p> <p>If this does not solve your problem please email me and I will set up a meeting so we can fully diagnose the error.</p> <p>Thanks,</p> <p>Sean Tracey<br /> <a href="mailto:stracey@progenygenetics.com">stracey@progenygenetics.com</a> </p> http://www.progenygenetics.com/community/topic/167#post-539 Thu, 01 Sep 2011 16:33:24 +0000 kai 539@http://www.progenygenetics.com/community/ <p>Hello all,<br /> When I try to import some new data into progeny, I set "pedigree name" and "UPN" as unique idenitfier. But when I import the data, just a part of of data can be imported.<br /> Do you know what the problem is? and how to solve the problem?<br /> Thanks,<br /> Kai </p> http://www.progenygenetics.com/community/topic/164#post-530 Mon, 08 Aug 2011 11:21:23 +0000 Sean 530@http://www.progenygenetics.com/community/ <p>Good question Melissa!</p> <p>While unfortunately there is no method in Progeny to apply password protection to an individual pedigree, you can apply read-only permissions to specific pedigrees.</p> <p>To accomplish this, you must first create a User Class for yourself. Select Administration from the top menu, then select User Maintenance. Choose Add Class, and name it. Then select your user name and check the box next to your newly-created user class to add yourself to it. Click Exit.</p> <p>Now right-click the pedigree in question and select Edit Pedigree Security. From this menu you can assign specific read and write permissions to specific User Classes. This will allow you to have full read/write access and give everyone else read-only or no permissions.</p> <p>Please email us at <a href="mailto:support@progenygenetics.com">support@progenygenetics.com</a> if you require more detailed instructions. </p> http://www.progenygenetics.com/community/topic/164#post-526 Wed, 03 Aug 2011 18:13:57 +0000 melissagilstrap@centura.org 526@http://www.progenygenetics.com/community/ <p>Is there a way to lock a pedigree so that it cannot be editted unless a password is entered or something like that? I would like to have an added security feature on my closed out cases so that they cannot be editted or accidently had features copied to them and have not been able to figure out how to do it. Any help would be appreciated! </p> http://www.progenygenetics.com/community/topic/86#post-520 Tue, 02 Aug 2011 09:47:53 +0000 David Odmark 520@http://www.progenygenetics.com/community/ <p>Hi freeseek,</p> <p>If you want to connect to the Progeny database using a CLI-based tool, and/or execute scripts on the database server itself from the command line in a "headless" Linux environment (i.e. where no X-windowing system can be presumed to be present), the best option is probably the 'dbisqlc' option that you mentioned above. This exe is located in the bin directory of the Progeny Linux server installation tree, and represents the "classic" version of the Sybase Interactive SQL UI. </p> <p>Documentation for this option can be found <a href="http://dcx.sybase.com/1100/en/dbadmin_en11/dbisqlc-interactive-dbutilities.html">here</a>. </p> http://www.progenygenetics.com/community/topic/150#post-515 Tue, 26 Jul 2011 09:29:56 +0000 Conrad Brammer 515@http://www.progenygenetics.com/community/ <p>Hello Kai, </p> <p>Would you be available to call support at 1-800-PROGENY (1-800-776-4369)? It would be much easier to resolve this issue that way and we can help you get your data moved over and offer suggestions on how you might like to store that data. </p> <p>On the surface, I am not sure if you want to have your data stored as flat fields, table rows or lookup table rows without understanding a bit more about the data. If you call support, you can just ask for me and I'll be able to assist. </p> <p>Thanks, </p> <p>Conrad </p> http://www.progenygenetics.com/community/topic/150#post-493 Fri, 15 Jul 2011 12:25:54 +0000 kai 493@http://www.progenygenetics.com/community/ <p>Hello,</p> <p>I'm new to use Progeny. </p> <p>I have a big table which contents 10 text fields and more than 2,000 rows.<br /> There are two fields existing in current Progeny DB. old_field1 and old_field2. The values of old_field1 + old_field2 are unique.<br /> The other 8 fields are new_field1 ..... new_field8. The 8 new fields need to be added in Progeny DB.</p> <p>The aim is based on the values of old_field1 and old_field2 to determine the other 8 new fields.<br /> The logical is: if old_field1=value1 and old_field2=value2, then new_field1=value3 ..... new_field8=value10.</p> <p>First, I tried to create 8 computed fields to handle new_field1 ..... new_field8. Then add the computed field definition in. But, I found the definition window cannot handle those many expressions.</p> <p>Then second, I tried to create a lookup table field to store the table. When I tried to import my big table into the file using lookup table maintenance, the name of the lookup table become the first column. I don't know if it is correct.</p> <p>Now, I stop and have no idea how to deal with this data.</p> <p>Do you know where the problem is and how to solve that? May be the lookup table is a way to solve the problem, but don’t know how to use it in DB yet.</p> <p>Thanks,</p> <p>Kai </p> http://www.progenygenetics.com/community/topic/86#post-492 Fri, 08 Jul 2011 09:26:37 +0000 freeseek 492@http://www.progenygenetics.com/community/ <p>I have recently upgraded to Progeny8 and installed SQL Anywhere 11.0.1.2519 from Progeny8LinuxServer.tar. Now I know three ways to access the server to run some SQL commands:<br /> jisql -S &lt;hostname&gt;:2638 -U progeny -P &lt;password&gt; (available from sybase jConnect)<br /> dbisqlc -c "uid=progeny;pwd=&lt;password&gt;;eng=Progeny;commlinks=tcpip{host=&lt;hostname&gt;:2638}" (available in Progeny8LinuxServer.tar)<br /> sqsh -S &lt;hostname&gt;:2638 -U progeny -P &lt;password&gt; (available open source)<br /> In Progeny8LinuxServer.tar there is also a dbisql program, which I assume is the sybase version of sqsh. I would like to try that but I think you forgot to include the isql.jar file with it because, when I run "dbisql -S &lt;hostname&gt;:2638 -U progeny -P &lt;password&gt;" I get "ERROR! This file could not be found: isql.jar".<br /> What other tools are there in the Server Software bundle? </p> http://www.progenygenetics.com/community/topic/86#post-489 Wed, 06 Jul 2011 15:15:38 +0000 Conrad Brammer 489@http://www.progenygenetics.com/community/ <p>We do have the tools available to do exactly what you describe as part of the Server Software bundle. The server software includes Sybase Central which allows you to connect to the back end of the database via ISQL. From this prompt you can run select statement queries, and modify tables. We don't recommend updating your data in this way, but it is possible. Do you have the server software or are you using a stand alone copy? </p> http://www.progenygenetics.com/community/topic/86#post-486 Fri, 01 Jul 2011 17:08:18 +0000 freeseek 486@http://www.progenygenetics.com/community/ <p>I have finally figured out how to fix the problem. I downloaded jConnect 6 from the sybase website:<br /> <a href="http://www.sybase.com/products/allproductsa-z/softwaredeveloperkit/jconnect" rel="nofollow">http://www.sybase.com/products/allproductsa-z/softwaredeveloperkit/jconnect</a><br /> After unpacking the file I understood that I only needed the files jisql.jar, jconn3.jar, and jisql to connect to the database with a command like the following (under UNIX):<br /> CLASSPATH=jisql.jar:jconn3.jar JAVA_HOME=/usr/lib/jvm/java-6-sun jisql -U progeny -P &lt;password&gt; -S jdbc:sybase:Tds:&lt;hostname&gt;:2638?ServiceName=progeny<br /> where &lt;password&gt; is the database administrator's password and hostname is the name of the computer where the database server is running. After successfully login, I only had to run the command:<br /> UPDATE st_data SET indname = f34;<br /> From what I understand, the st_data is the database table with almost all the information and the indname column is the "Individual name" field. In my case f34 was an additional column with the entries we had in the database that we actually wanted as "Individual name" entries. To know what fieldname corresponds to column f34 is enough to run the command:<br /> SELECT fieldname FROM st_datadictionary WHERE fieldid = 34 (try for a full description SELECT * FROM st_datadictionary)<br /> I think there should be also a way to perform the same operations from the command line using the open source command sqsh or isql from sybase, but I have not been successful so far. I actually would appreciate this option as it would allow me to query the database also when I am not in the lab. I tried to run<br /> sqsh -U progeny -P &lt;password&gt; -S jdbc:sybase:Tds:&lt;hostname&gt;:2638?ServiceName=progeny<br /> but nothing happens. I cannot find a tutorial on how to use sqsh online. It seems to assume that you already know how to use isql from sybase. Any suggestions? </p> http://www.progenygenetics.com/community/topic/86#post-475 Mon, 13 Jun 2011 14:18:15 +0000 freeseek 475@http://www.progenygenetics.com/community/ <p>Thanks for the offer. Unfortunately we are not allowed to share the database outside of our research area, as this would be in violation of the confidentiality agreement. I do assume that it should be possible to change the values by connecting directly to the Sybase database. I will try that. </p> http://www.progenygenetics.com/community/topic/86#post-474 Fri, 10 Jun 2011 16:54:06 +0000 Conrad Brammer 474@http://www.progenygenetics.com/community/ <p>The import module actually does update system fields, but only certain ones. The ones you can update show up in the right click menu when you right click on the column headers. In the case of an 'Individuals' import, however, there are only two that can be updated via the Import Module: "Gender" and "Deceased" </p> <p>If you are currently covered under PSP (Progeny Support Plan), we can do this for you as a free service for all current members. To do so, simply contact general support and give them your Customer Number. We will set up a secured account folder for you on our FTP site for you to post your database, and we can update your individual names and re-post the database back into your account folder. </p> <p>Since Individual Name is the unique identifier for the Individual Import, it is currently not possible to update that value using the Import Module. </p> http://www.progenygenetics.com/community/topic/86#post-472 Fri, 10 Jun 2011 15:54:03 +0000 freeseek 472@http://www.progenygenetics.com/community/ <p>I need to change the "Individual name" for about 10,000 individuals in my database. I wanted to use the import feature by matching the "Global ID" but it seems like the import function does not allow me to change system fields, despite the fact that I could not find mention of this problem in the help. Do I really have to change each each sample's "Individual name" manually? This seems very painful. Can you suggest something? </p> http://www.progenygenetics.com/community/topic/139#post-454 Fri, 13 May 2011 14:35:14 +0000 David DeRam 454@http://www.progenygenetics.com/community/ <p>The status of the BRCAPRO license should be determined soon.</p> <p>We will work to reproduce the issue that you are having with BRCA1 test results and be in touch with you.</p> <p>Thank you. </p> http://www.progenygenetics.com/community/topic/143#post-453 Fri, 13 May 2011 08:12:12 +0000 Conrad Brammer 453@http://www.progenygenetics.com/community/ <p>Hello Manuel, </p> <p>We would need to to call our support line, 1-800-PROGENY (1-800-776-4369) or email us at <a href="mailto:support@progenygenetics.com">support@progenygenetics.com</a>? We would need to take a look at this issue to figure out what the problem is. </p> <p>Thanks, </p> <p>Conrad </p> http://www.progenygenetics.com/community/topic/143#post-452 Thu, 12 May 2011 18:22:29 +0000 Manuel Teixeira 452@http://www.progenygenetics.com/community/ <p>Hi.<br /> I use the "Patient ID #" field with the format IPO- followed by 8 numbers, e.g., IPO-12345678. When I had this field to a Individual data spreadsheet all patients appear with "Invalid DateTime" instead of their respective IPO-number, so I am not able to export the data from this field. This strange because this is a text field. Any help? Thanks.<br /> Manuel </p> http://www.progenygenetics.com/community/topic/139#post-451 Thu, 12 May 2011 18:10:58 +0000 Manuel Teixeira 451@http://www.progenygenetics.com/community/ <p>Dear David,</p> <p>Thanks for your feedback regarding the IP address that is used for BRCAPRO web service. The web service is still operating at least with version 8.01.01. I hope Progeny solves the license issue because it would be really useful to be able to use it from Progeny (I have a license for the stand alone BRCAPRO, but it is too cumbersome to enter the pedigree twice.</p> <p>Regarding issue #2, I am sorry but in my hands the cancer risk calculation (the text that is pasted to the pedigree) and the probability carrier/BRCA1/BRCA2 calculations stay the same irrespective of what I enter in the field "BRCA1 test results" in the BRCA tab: "no test", "positive" or negative". This is true with my database with the same BRCA tab that have used from the demo db, as well as using the demo db itself with the cancer pedigree or a new pedigree.<br /> I hope I will be able to use this feature in the future.</p> <p>Best regards,<br /> Manuel </p> http://www.progenygenetics.com/community/topic/139#post-443 Tue, 10 May 2011 15:00:39 +0000 David DeRam 443@http://www.progenygenetics.com/community/ <p>Please note that the BRCAPRO web service has recently changed their licensing model and it is possible that you may no longer be able to connect to their web service. I will provide answers to your questions above in the case that is not a problem.</p> <p>(#1 above) - If you are able to connect through the wireless internet connection but not the wired connection then it is likely that you have an issue with the firewall. Please be sure you can connect to <a href="http://155.52.219.205:8080/" rel="nofollow">http://155.52.219.205:8080/</a> (not <a href="http://bayesmendel.dfci.harvard.edu/risk/)" rel="nofollow">http://bayesmendel.dfci.harvard.edu/risk/)</a>.</p> <p>(#2 above) - Are you working with the demo database? We are not seeing a problem with the demo database that ships with Progeny. Changing BRACA1 test results and BRCA2 test results does impact the calculations. Please let us know if you are using the demo database and if not please let us know how you have your fields setup.</p> <p>Thank you. </p> http://www.progenygenetics.com/community/topic/139#post-432 Sat, 07 May 2011 13:20:02 +0000 Manuel Teixeira 432@http://www.progenygenetics.com/community/ <p>Hi.</p> <p>I have two issues with BRCA analysis in Progeny8.</p> <p>1- There is an issue with risk calculation using my wired web connection at work with a proxy server (it works perfectly at home and using a wireless internet connection). I contacted my Informatics department and they allowed access to the web address <a href="http://bayesmendel.dfci.harvard.edu/risk/" rel="nofollow">http://bayesmendel.dfci.harvard.edu/risk/</a> without going through the firewall, but still no success. It is not evident in the program menus how to set up a proxy in Progeny. I think that Progeny8 has a problem to access the internet via a proxy server that did not existed with Progeny7, because when I start the program not even the Progeny logo and the banner appear in the login window. This does not happen with Progeny8 when I use the laptop at home and it did not happen before with Progeny7 at work. Any help with this?</p> <p>2- I have tested the web risk calculation (using my private wireless internet access) and it works fine for calculating the mutation probability. However, the disease risk and mutation probability calculation is the same irrespective of indicating in the BRCA tab whether or not a mutation has been found in the family. This works correctly in CaGene. It seems like the information in the fields "BRCA1 test results" and "BRCA2 test results" are not taken into account in the calculation. Is this being corrected?</p> <p>Looking forward for your feedback, I send you my best regards,<br /> Manuel </p> http://www.progenygenetics.com/community/topic/128#post-409 Thu, 21 Apr 2011 04:21:41 +0000 rmorrison100 409@http://www.progenygenetics.com/community/ <p>Thanks. Got the solution to this problem now. Thanks again.<br /> <a href="http://diyhometools.com/makita-bdf452hw-18v/">Makita Drill Review</a> | <a href="http://www.singorama.com/articles/vocal-exercises">Vocal Exercises</a> </p> http://www.progenygenetics.com/community/topic/128#post-405 Sun, 17 Apr 2011 12:18:02 +0000 rmorrison100 405@http://www.progenygenetics.com/community/ <p>Thank you. I got the same problem few days ago. </p>