Team:Imperial College/Software
A.L.I.C.E was developed concurrently with G.E.A.R. to facilitate the design and optimization of co-cultures. On this platform, synthetic biologists can submit entries containing growth conditions, protocol and data for cell cultures. Submitted entries can also be searched to find that species have previously been grown together in a co-culture or may possibly be grown together in a co-culture due to similarities in their growth patterns and conditions. See below for a walkthrough of A.L.I.C.E.
A.L.I.C.E allows synthetic biologists to gauge how species will grow in certain external conditions, potentially allowing scientists to control the population ratio of species in a co-culture via control of these external conditions, such as temperature and pH. The growth characteristics of cell cultures can be tuned externally based off of insight gained from A.L.I.C.E.
Furthermore, by incorporating growth data of species from A.L.I.C.E into population-level models of co-cultures containing the GEAR system, it will be possible to predict how the GEAR system will affect the population-level behavior of a co-culture of these species. This will then allow the GEAR system to be optimized to tune the population ratio of these specific species.
Figure 1: Growth data on species searched and retrieved via ALICE
Walkthrough Documentation
To search for species to co-culture together, you will first be directed to this page:
Simply enter the names of the species you are looking to culture together. The population fields must be filled in and begin with a single capitalized letter for an abbreviated genus followed by the species or strain name (eg. E. coli) to successfully run a search. When typing into these fields a drop-down, autocomplete list of suggestions of species previously entered to ALICE will appear.
Relevant co-culture entries will appear first after the search is executed. This will be followed by relevant monoculture entries ordered by first ascending doubling time. If doubling times are the same, monocultures will be ordered by ascending temperature and then by ascending pH. Finally, an option to search again will be found at the bottom of results:
If no relevant co-cultures can be found, you will be notified and no co-culture entries will be displayed. If no relevant monocultures are found for a species, none will be displayed, and you will also be notified. If no monocultures of either species can be found, nothing will be displayed for either species, and you will be notified of this for both of them. However, if monocultures of one species are found, these will still be displayed.
The submission page for monoculture entries will display the following entry form:
There is extensive validation of the fields of this submission form. You will not be able to submit an entry until all required fields are completed. Only valid values or numbers can be entered into numerical fields such as temperature, doubling time and pH. Additionally, the species field must begin with a single capitalized letter for an abbreviated genus followed by the species or strain name (eg. E. coli). When typing into the species field a drop-down, autocomplete list of suggestions of species previously entered to ALICE will appear. Finally, the entry will only be successfully submitted if the URL field is filled in with a valid Google spreadsheet URL.
In order for your optical density data spreadsheet obtained from experiments to be displayed correctly as a graph when your submitted entry is searched up, please follow the instructions on this page form correctly, especially with respect to never deleting or changing the Google spreadsheet's location after submission and the correct configuration of the spreadsheet:
The top-left cell of the sheet WILL NOT affect what is displayed in the graph at all. The left-most column will contain the time points (in minutes) of the x-axis. Each column to the right will contain optical density measurements that will be plotted for each time point, as part of a single growth curve. The first row of these columns contains the labels in the legend for each growth curve.
When submitting an entry ensure the Google spreadsheet this URL links to is shared so that anyone with the link can view it and that the optical density data obtained from experiments is formatted correctly. When monoculture entries are displayed, the graphs that are displayed with entries that are searched up are created from the Google spreadsheet data in the Google spreadsheet URL that was submitted with each monoculture entry.
The following submission form will be displayed on the page to submit co-culture entries:
There is extensive validation of the fields of this submission form as well. You will not be able to submit an entry until all required fields are completed and valid. Only numbers can be entered into numerical fields such as temperature, doubling time, pH, inoculation ratio, hours of stable population ratio and hours after which population 1 was inoculated. All these fields apart from temperature must be positive numbers, and only numbers greater than 1 can be entered into the inoculation ratio field. Additionally, the population fields must begin with a single capitalized letter for an abbreviated genus followed by the species or strain name (eg. E. coli). When typing into these fields a drop-down, autocomplete list of suggestions of species previously entered to ALICE will appear.
As there are a multitude of ways to measure co-culture growth, data is not required to be submitted with a co-culture entry. However, an image file uploaded online at MediaFire can be optionally submitted to visualize growth data for an entry. To do this, include a valid URL of a direct link to an image file uploaded on MediaFire on the appropriate field of your submission form.
To get the direct link URL of an image uploaded on MediaFire, simply click on the image file, click share and click for more sharing options to copy its direct link URL. The corresponding image of this URL will be displayed along with the protocol and growth conditions of a co-culture entry when the entry is searched up. Again, the file's location should not be changed after its URL is submitted.
As of mid-September 2016, the Safari web browser developed by Apple does not support many important features of html and is therefore incompatible with ALICE. If accessed via Safari, search and submit features on ALICE will be blocked and unusable:
To access A.L.I.C.E, click and navigate on the banner above or click HERE!
The source code, files and most recent backup of A.L.I.C.E are stored on Github HERE!
Alternatively, click HERE to download directly!
