"Excellet Steve, thanks for all the info. Much appreciated as usual!
Please let us know about the MySQL FIMS as early as possible (we would happily beta test) since our LabDB is based on MySQL, and if we could directly tap into it without having to…"
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Franck Stefani
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- Melbourne, VIC
- Australia
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Gert Woerheide replied to Franck Stefani's discussion 'Using Biocode' in the group Biocode LIMS plugin
Steven Stones-Havas replied to Franck Stefani's discussion 'Using Biocode' in the group Biocode LIMS plugin"Hi there Gert,
FIMS/LIMS data is attached to your sequences when you annotate them using the function, or download the traces from the LIMS. Those fields and values will stay on your sequences until you run the annotate function again,…"
Gert Woerheide replied to Franck Stefani's discussion 'Using Biocode' in the group Biocode LIMS plugin"hi there, is it possible (and without danger) to use different Excel FIMS? We have one for a large barcoding batch of external samples (about 17,000) and one for the general lab use (a couple of thousand samples). Is the FIMS data saved in the LIMS…"
Franck Stefani replied to Conrad Schoch's discussion 'Homopolymeric bases problem' in the group Fungi"Hi,
I think this paper provides a good set of solutions against polymerase slippage:
http://www.biotechniques.com/multimedia/archive/00087/BTN_A_000113369_O_87854a.pdf
Franck"
Franck Stefani replied to Conrad Schoch's discussion 'Homopolymeric bases problem' in the group Fungi"Some solutions are suggested here: http://pan.stanford.edu/section_html/DNASEQ/analysis.html"
Franck Stefani replied to Conrad Schoch's discussion 'Homopolymeric bases problem' in the group Fungi"Hi there,
I am facing polymerase slippage with Dermocybe specimens (40% of my ITS sequences are messy...) because of the presence of poly-T or poly-G either in the ITS1 or 2. Until now, I have used the primer sets ITS1-F/ITS4 or ITS1-F/ITS4b…"
Steven Stones-Havas replied to Franck Stefani's discussion 'Using Biocode' in the group Biocode LIMS plugin"Edit history is something else we've considered. It's not implemented now, but it's one of our long-term goals (along with properly dealing with security and multiple user accounts, so that the history can be recorded against…"
Gert Woerheide replied to Franck Stefani's discussion 'Using Biocode' in the group Biocode LIMS plugin"One thing I just noted is the History field for each item created. What is this currently used for? It does not really display the history of the item, i.e. for an extraction plate it should show who created the plate and when, and then subsequent…"
Steven Stones-Havas replied to Franck Stefani's discussion 'Using Biocode' in the group Biocode LIMS plugin"Hi there guys,
You can delete plates in the LIMS, but not workflows (deleting extraction plates deletes all workflows associated with those extractions though). Just search for the plates you want to delete, select them, and hit the…"
Franck Stefani commented on Steven Stones-Havas's group 'Biocode LIMS plugin'"Hi Steven,
I am used to set up my PCR reactions in strips of 8 wells (as Gert seems to do...) when I plan to amplify less than 48 samples. Over 48 samples I shift to a plate. Maybe the PCR reaction in biocode should be displayed in X columns…"
Franck Stefani commented on Steven Stones-Havas's group 'Biocode LIMS plugin'"Hi,
I am trying to create a PCR reaction with 28 individual reactions. But then the "New PCR" window does not offer more than 24 wells. It sounds like PCR reaction with a number of individual reactions ranging from 25 to 47 can not…"
Gert Woerheide replied to Franck Stefani's discussion 'Using Biocode' in the group Biocode LIMS plugin"Hi there,
I can not answer the question of how to delete a workflow, but my question goes even further.
We have set up our LIMS with multiple usernames.
If user A (logged in to LIMS under user A) now creates an extraction-plate, will user B (logged…"
Franck Stefani replied to Franck Stefani's discussion 'Using Biocode' in the group Biocode LIMS plugin"Ok I found by myself the answer to my second question. Modify the names in your excel spreadsheet, logout and login Biocode, It is re-downloading your excel spreadsheet with your corrections...
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Franck Stefani added a discussion to the group Biocode LIMS plugin
Using Biocode
Hi there, I am playing with Biocode, just to try to figure out if it is flexible enough to fit my work. I have two questions: - How could we erase some workflows wrongly created?- How could we modify the species names associated with tissue_id if mistakes were done while typing their name? FranckSee More
Franck Stefani joined Steven Stones-Havas's groupBiocode LIMS plugin
The Biocode LIMS plugin is a free suite of plugins to Geneious that allow you to track and manage your entire lab workflow, from tissue samples through to Sequence analysis and Genbank Submission. Visit our website to download the plugins.See More
Profile Information
- Institution/Organization
- Royal Botanic Gardens - Melbourne
- Title/Position
- Postdoctoral fellow
- I’m involved in, or am interested in the following barcoding initiatives
- DNA Barcoding Initiative for Conservation, Database Working Group, Data Analysis Working Group
- I’m involved in or interested in the following iBOL Working Groups
- WG1.3 Fungi
- Keywords about my barcoding projects (separate each choice with a comma)
- Dermocybe, Cortinarius, high throughput sequencing
- 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
- Current Project(s)
- Molecular phylogeny and barcoding of Australian Cortinarius subg. Dermocybe
Comment Wall (1 comment)
- At 8:23am on November 30, 2010,
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