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Biocode 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.

Website: http://software.mooreabiocode.org
Location: Moorea, French Polynesia
Members: 51
Latest Activity: Jun 2

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, 2013.

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, 2013.

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.

My Comment Wall

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Comment by Steven Stones-Havas on December 19, 2012 at 11:32pm

Hi Guys,

We've just released a new version of the plugin designed to work with the new Google Fusion Tables API.  Google are turning off the old API on January 15, so if you are using Fusion Tables make sure you upgrade your plugin by then.

This update also addresses some issues discussed on this forum - most notably the problems that some users were having marking their assemblies as passed, and the problem some people were having annotating their sequences with FIMS data from an excel sheet.

You can download the new plugin at http://software.mooreabiocode.org

Comment by Steven Stones-Havas on November 15, 2012 at 12:31am

Hi there Suzanne,

Unfortunately there isn't a way to bulk remove traces from a plate.  The only way to do this would be to delete the plate, and create it again.  We are looking to add this feature pretty soon though, as it has been requested before.

Comment by Ruth Castillo on October 29, 2012 at 10:36am

Hi, I have started working with the biocode plugin since a week ago and I find it awesome, and I am looking forward to use it further. Everything worked as in the tutorial video (except for the binning parameters, but I already read how to solve that) when I used it with an excel table in a local database... However, I would like to use the google fusion tables possibility. I have tried to do the same, and my tables are recognized in the login window, however when I entered into the login, nothing is recognized when I do the search as if anything was imported... Can anyone explain me what I could possibly be doing wrong? Thanks A LOT for your answer,

Best greetings,

Ruth

Comment by Suzanne Nagi on September 18, 2012 at 3:31pm

Hi,

Is there a way to bulk remove traces? I added my trace files to several plates twice and now have repeat sequence entries which are slowing down the analysis. Is there any way to efficiently get rid of these on a plate by plate basis?

Comment by Steven Stones-Havas on July 18, 2012 at 2:58am

Hi there Oliver.  The consensus sequences are returned in searches of your Biocode lims - just check the "sequences" checkbox when you do your search.  You can also refine your search to include just passed ones, then you can select them all, and export as FASTA (or any other format that Geneious supports), or submit them to Genbank

Comment by Oliver berry on July 3, 2012 at 10:34pm

Hi,

I have a question regarding export of a final list of passed sequences for downstream analysis.  In some cases I only have forward sequences, whilst in others I have a consensus of fwd & rev. I've passed the high quality consensus sequences, and the high quality forward sequences. I'd like to know the best way to gather these together and export them as a single package of sequences?  Sorry if this is obvious, but I'm unsure about whether failed consensus sequences that have a corresponding passed forward sequence (i.e. the reverse sequence only failed) are treated, and I want to use all passed data. Cheers.

Comment by Steven Stones-Havas on July 1, 2012 at 6:39pm

Hi Oliver,

Thanks for the feedback - it's great to know that people are finding our software useful!  Set binning parameters is still under the sequence menu, but you probably do not have per folder/document binning turned on.  To do that, go to tools-> preferences and click on the sequencing tab.  Make sure that the "Enable per folder/document binning" checkbox is checked and then you should find what you're looking for at the very bottom of the sequence menu.

thanks

Steve

Comment by Oliver berry on June 29, 2012 at 4:03am

Hi,

Very impressed with the Biocode plugin so far.  The video demonstration is a big help.  One discrepancy I've noticed is that I can't find the "set binning parameters" option under the Sequence menu.  Seems like this is a recent change. Does anybody know how to set binning parameters? Cheers

Comment by Steven Stones-Havas on December 23, 2011 at 4:53pm

Hi Gert,

 

Publishing the documentation is one of the things that got interrupted by the holidays - I'm in the process of publishing it here: http://software.mooreabiocode.org/index.php?title=Reporting but I'm having some trouble with the screenshots.  I'll put up as much as I can by the end of today, but I suggest that the best way to learn is to have a play with it.  If there's something in particular that you would like to get reporting on, and you can't figure out how to do it, please let me know!

 

Merry Christmas!

Comment by Gert Woerheide on December 22, 2011 at 3:08am

Very cool, Steve, great job!

Is there some detailed documentation about the new features? E.g. the reporting function etc.? Nice little status button btw (red/green), well done... 

 

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