Team:Aachen/Practices/tubefront


Introduction

If you ask iGEM veterans about the organization of their freezers, you often get the same anwer: "chaotic". What if iGEMers would always know where to put and find their samples? Two organization paradigms are most popular:

  • organization by type — e.g. putting all primers in one box
  • organization by purpose/person — e.g. everything related to the kill switch in one box

But both of these paradigms lead to the same problem: For good scientific practice many parameters must be recorded. In most cases, this includes date, name, insert, backbone, strain, clone number, medium and sometimes even the growth medium.

“

All this has to be scribbled in very small, and hopefully permanent penmanship on the top of the tube, which is a circle about 1cm in diameter. [...] It's an organizational nightmare held together by a very thin thread of paperwork.

”

Jeff Shrager, Ph.D, 14th July 2000[1]

When teams and projects grow, the number of samples steadily increases and at some point people tend to loose control and oversight. Freezers are collapsing under highly frequent usage and samples get lost. For iGEM teams this typically results in nightly phone calls to find stuff and match the project deadline. In 2014 we had many of these troubles and knew something had to change so we could scale up.

Therefore we developed and deployed a mobile-first sample management system for humans. It solves the problem of sample identification and tracking without the need for expensive equipment.

Aachen tubefront-logo.png

  • does not require additional equipment
  • thoroughly tested integration with the wiki documentation
  • reduces cost and workload by avoiding redundancies

a

For the time of the Jamboree, we are opening the gates to the tubefront instance of iGEM Aachen. Feel free to visit and browse our sample inventory at http://tubefront.com/public/iGEM_Aachen.

Alternatively you can visit http://tubefront.com/Demo and log in with "demouser" and "password" to try editing yourself!

We have used tubefront throughout the project and accumulated some basic statistics showing how it was used:

Aachen PracticesTubefrontStats.png
Total Samples During iGEM 2015
In the beginning several samples from the previous year were added. Over the course of iGEM 2015, we have generated new samples at a rate of approximately 15.5 samples/day.

Interface

In the pictures below you can see how tubefront looks like on a mobile device. Of course, you can also use it on your laptop.

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Aachen tubefrontHelp1.png
Sample information on a mobile device
Container types and states are saved alongside the box and slot within the freezer. The layout is optimized for single-handed use.
Aachen tubefrontHelp2.png
Additional Metadata
A description field allows for detailed information about samples. with the box preview it is easy to quickly locate the tube.

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By adding tags, you can add more information that can also be filtered by in the search function.

Tips and Tricks

Our experience shows that you should use tubefront-IDs for almost any sample/container that is stored for more than two days. This includes for example cryos of different clones, purified plasmids, purified PCR products etc.

Tubes that are too small to be labeled, such as PCR tubes can be stored together with their siblings in 15-50 ml tubes.

Aachen tubefrontHelp3.png
Storage of PCR tubes
PCR tubes are best kept inside a falcon tube that has its own ID.

Short box names are better, because then you can easily write ID, box and slot (eg. XE3D P':B7) on a post-it before going to the freezer.

We use tubefront IDs for the primers in our cloning software and for ordering. Upon arrival the 100 μM stocks go into our boxes P or Q, while the 10/20 μM dilutions go into the same positions in boxes P' or Q'.

In our survey on lab organization, we also collected advice for newcomer teams. Make sure to take a look at the survey results.

MediaWiki Integration

To integrate tubefront with your MediaWiki, create a new MediaWiki-Template with the name "tubefront". Paste this code into the template:

<html>
    <!-- jQuery -->
    <script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.1/jquery.min.js"></script>

    <!-- tubefront integration script for group "iGEM_Aachen" -->
    <script>
        $('p').each(function () {
            var templ = '<a href="http://tubefront.com/iGEM_Aachen/editcontainer.php?id=$1" onmouseover="loadTooltip(this,' + "'$1'" + ')">$1</a>';
            var replaced = $('body').html().replace(/#(\S*)#/g, templ);
            $('body').html(replaced);
            return false;
        });
        function loadTooltip(el, containerid) {
            $.get("http://tubefront.com/getinfo.php", { group: "iGEM_Aachen", containerid: containerid }).done(function( data ) {
                el.title = data;
            });
        }
    </script>
</html>


On any wiki page, type # before and after an ID and call the template on the bottom of the page once.

Aachen tubefrontHelp4.png
Wiki integration
The tubefront integration template is included once at the bottom of a wiki page. tubefront IDs are marked with two # symbols.

References

  1. ↑ Jeff Shrager - Diary of an Insane Cell Mechanic http://jeffshrager.org/diary/diary.html


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