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Biocode LIMS plugin

Information

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.

Website: http://software.mooreabiocode.org
Location: Moorea, French Polynesia
Members: 49
Latest Activity: Apr 10

Introduction

Hi guys,

We intend this group to be the hub of our communication with the barcoding community. We are extremely proud of the Biocode Plugin, but we don't expect it to be perfect from the first release. If you have a problem, a question, or a suggestion about how we can make our plugin better, please start a thread in the discussion forum. Alternatively, you can email us at support@mooreabiocode.org.

Happy Barcoding!

Discussion Forum

double columns 1 Reply

Hi there,I have a little problem here and would need help. I updated the biocode plugin to the latest version, reset the FIMS connection and chose the table columns again. All is working fine, except…Continue

Started by Matthias Geiger. Last reply by André Schütte Apr 10.

Query Taxon 4 Replies

Hi. When I download traces from lims a large % of my sequences get assigned to the same (and mostly incorrect) genus - specifically "Sclerolobium sp. A PP" - in the organism column. Is there any way…Continue

Started by Suzanne Nagi. Last reply by Suzanne Nagi Jan 2.

Working with Fusion Tables 2 Replies

Hi,I realized I posted my comment in the wrong place... Apologies, here it goes again:I have started working with the biocode plugin since a week ago and I find it awesome, and I am looking forward…Continue

Started by Ruth Castillo. Last reply by Ruth Castillo Nov 15, 2012.

cannot connect to LIMS 1 Reply

Hello, My name is Oliver Wooley and im a PhD student at the Australian Centre for Ancient DNA (ACAD) in Adelaide. I am looking into the setting up a LIMS system for our lab but have not been able to…Continue

Started by oliver wooley. Last reply by Steven Stones-Havas Oct 10, 2012.

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My Comment Wall

Comment

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Comment by Steven Stones-Havas on December 22, 2011 at 12:35am: Hi guys, We've just released version 2.3.0 of the plugin. It contains a lot of requested features, as well as a reporting and charting module. Check it out at http://software.mooreabiocode.org

Comment by Steven Stones-Havas on November 10, 2011 at 9:18pm: Hi guys, I've added the extra field to PCR and Sequencing reactions. check the january thread for details

Comment by Gert Woerheide on November 10, 2011 at 4:15am: Yes, something like this has already been requested in January!

Comment by Steven Stones-Havas on November 10, 2011 at 3:26am: Hi there James,

That's an interesting problem. Perhaps we could have an extra reaction state, that sits in between pass and fail (much like the medium bin that we use for sequence binning in Geneious). I would rather call it something more generic than "resequence" though. How about "low quality" to indicate that there is a sequence present, but it isn't of sufficient quality?

Comment by James Kitson on November 9, 2011 at 7:15am: Hi Steven,

Most of the time I get pretty good sequence by only sequencing forward but occasionally I need to reverse sequence to get the end of my fragment. Currently I mark these in the LIMS as fails so that Biocode can make plates and lists etc automatically but I also do this for PCRs/sequencing reactions that have failed completely. This has the problem then that complete fails are then mixed in with samples that only need to be resequenced. Can you think of a way of getting Geneious to differentiate between the two scenarios or can we have an additional "resequence" reaction state added in future versions?

Thanks,

James

Comment by Steven Stones-Havas on May 13, 2011 at 2:27am: Hi guys,

I'm pleased to announce the release of the Moorea Biocode plugin version 2.1! To see the exciting new features we've added, and to get yourself a copy, visit http://software.mooreabiocode.org

Comment by Steven Stones-Havas on January 24, 2011 at 10:35am: It would be pretty simple to add an extra option for strips, where you could choose X strips to produce an 8 by X plate. I think that should meet your needs.

Comment by Franck Stefani on January 24, 2011 at 8:02am: 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 (x<6) of 8 rows each, for PCR reactions with less than 48 samples. But I really do not know how much complex this could be for you to make theses changes.

Comment by Gert Woerheide on January 24, 2011 at 1:47am: We regularly set up reactions in strips (8 wells). Would it be possible to get an option also for this?

Comment by Steven Stones-Havas on January 24, 2011 at 12:13am: Hi Franck,

You are correct - we allow a limited number of individual reactions to be created at once. The reason for this is that it is a little hard to display large numbers of individual reactions in a way that's easy to view onscreen. Most people I have seen who run reactions in tubes run less than ten of them at once, so your case is different to what I have seen before. Could you explain your lab workflow to me a little to help me better understand how to improve the plugin for you?