"Dear Steve,
We are currently facing exactly the same problem. Is there any solution around?
Best wishes,
Guy
"
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Dirk Erpenbeck's Page
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Guy Colling replied to Dirk Erpenbeck's discussion 'Dealing with old barcoding data' in the group Biocode LIMS plugin
Dirk Erpenbeck replied to Dirk Erpenbeck's discussion 'Deleting plates' in the group Biocode LIMS plugin"Great! We used v. 8 to create the database and recently upgraded to v. 9
I hope that helps,
Thanks a lot,
Dirk
"
Dirk Erpenbeck replied to Dirk Erpenbeck's discussion 'Dealing with old barcoding data' in the group Biocode LIMS plugin"Hi Steve,
back on this issue -
First thanks for the information, but the problem remains. I tried several approaches (annotatad traces, raw traces etc and followed your suggestion and the workflow shown in the video-tutorial). When I use…"
Steven Stones-Havas replied to Dirk Erpenbeck's discussion 'Deleting plates' in the group Biocode LIMS plugin"Thanks, Dirk. I'll write you the script tomorrow.
Do you have any idea what version of the database script you used to create your remote database, and how many times (if any) it has been upgraded to a newer version?
thanks
Steve"
Dirk Erpenbeck replied to Dirk Erpenbeck's discussion 'Deleting plates' in the group Biocode LIMS plugin"Hi Steve,
that would be great! Our LIMS is on a remote MySQL database. Deleting the plates individually does not work either - I get the same error messages.
Looking very forward to the new release! We have a lot of data piling up.
Best,…"
Steven Stones-Havas replied to Dirk Erpenbeck's discussion 'Deleting plates' in the group Biocode LIMS plugin"Hi Dirk,
That looks like a bug - could you tell me what type of LIMS database you're using (local or remote). It looks like the LIMS is having trouble deleting traces associated with the sequencing plate you're deleting - the only…"
Dirk Erpenbeck added a discussion to the group Biocode LIMS plugin
Deleting plates
Hi Steve,Me again - I'm trying to delete some test plates from the LIMS and get (for some of them) the attached error message. Any tips how to proceed?Thanks a lot and best regards,DirkP.S. Did you succeed finding a solution for our problem that each time we start biocode we have to specify all fields for tissues,…See More
Franck Stefani replied to Dirk Erpenbeck's discussion 'Primer list issue' in the group Biocode LIMS plugin"Hi Dirk,
Yes that was helpful to fix the never-ending indexing. Thanks
Franck"
Dirk Erpenbeck replied to Dirk Erpenbeck's discussion 'Primer list issue' in the group Biocode LIMS plugin"Hi Franck,
It was just a corrupted document that couldn't be indexed. If I remember correctly you can click on the index - wheel (or somewhere else down there) to get the details on the document that cannot be indexed. Just delete this…"
Franck Stefani replied to Dirk Erpenbeck's discussion 'Primer list issue' in the group Biocode LIMS plugin"Hi Dirk,
I have got the same problem. How did you fix it?
Cheers,
Franck"
Steven Stones-Havas replied to Dirk Erpenbeck's discussion 'Dealing with old barcoding data' in the group Biocode LIMS plugin"Hi Dirk,
Marking an assembly as passed should result in a single sequence (the consensus sequence of that assembly). The traces never appear in the search results directly - they appear in the plates themselves (double click on a well and…"
Dirk Erpenbeck replied to Dirk Erpenbeck's discussion 'Dealing with old barcoding data' in the group Biocode LIMS plugin"Hi Steve,
Thanks for your quick answer again!
Here's a new question again (you see we are VERY busy with your program) for which you might have a logic answer:
When I assemble sequences and would like to upload them to the LIMS as…"
Steven Stones-Havas replied to Dirk Erpenbeck's discussion 'Dealing with old barcoding data' in the group Biocode LIMS plugin"Hi Dirk,
Our recommended protocol is to bulk load your traces onto the plates first, then download them from the plates into Geneious as that makes sure that the traces are correctly annotated with the LIMS and FIMS information. You can do it…"
Dirk Erpenbeck replied to Dirk Erpenbeck's discussion 'Dealing with old barcoding data' in the group Biocode LIMS plugin"Hi Steve,
Cool, we finally got to this problem and it works. I like the "bulk editor" function for our folders of .abi traces, however, do I see it correctly that when I want to use "Bulk add traces" for cycle sequencing…"
Gert Woerheide replied to Dirk Erpenbeck's discussion 'Verify Taxonomy columns' in the group Biocode LIMS plugin"Hi Steve,
thanks, "connect at start up" solves the driver problem, but the issue with the error report on the connection to the FIMS (see Dirk on May 31, 2012 at 9:39am above) still persists. Can't wait for the fit ;-)
Keep…"
Profile Information
- Institution/Organization
- LMU Munich
- Title/Position
- Researcher/Faculty member
- Website
- http://www.gwdg.de/~derpenb
- I’m involved in, or am interested in the following barcoding initiatives
- Marine Barcode of Life (MarBOL), Data Analysis Working Group
- Keywords about my barcoding projects (separate each choice with a comma)
- Sponge Barcoding Project
- I’m involved in the following aspects of barcoding:
- Fieldwork/specimen collecting, Museum work/specimen curation, Labwork/generating barcode sequences, Management of barcode data, Analysis of barcode data, Using barcode data in taxonomy/systematic biology, Using barcode data for other applications, Organizing/managing barcoding projects, Science policy related to barcoding
- Current Project(s)
- Sponge Barcoding Project, www.spongebarcoding.org ;
Sponge Genetree Server, www.spongegenetrees.org
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