To submit entries to A. L. I. C. E, you will need to enter the access password correctly ONCE:





After clicking to obtain permission, you will be redirected to the instructions you need to follow after verifying you are human:



After proving you are human, you will be instructions on how to request permission to submit entries:



The reply you receive should contain the access password. Assuming this is entered correctly, you will now have access to the pages to submit entries.

Upon entering the correct password, the submission page for monoculture entries will now 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.

Upon entering the correct password, the following submission form will now 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.

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 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.

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 use VESICLES, you must have already installed:

Next, download VESICLES-master HERE!
Alternatively, download from Github HERE!

Unzip the folder. You are now ready to start using VESICLES.

To add DNA sequences to the parts list:

Open the VESICLES-master folder. Double-click and open save2partslist.R with RStudio. Run the script. In Rstudio, using the keyboard shortcut CTRL+ALT+R does this. Alternatively you can click through the menu bar.



Next, at the bottom of the R Console, type: save2partslist("the part's name","the sequence"). The sequence can be copied and pasted in, but please note the quotation marks must be included. Now hit enter:



All whitespace will be removed from the sequence, and all lowercase letters will be capitalized before it is added into a file in VESICLES-master called partslist.txt



NOTE: The partslist.txt file will be created if none already exists in the VESICLES-master folder. Otherwise, new entries will be added to this file.

Additionally, you will not be able to add parts to this list if invalid DNA characters are contained in the sequence (ie. anything other than A, T, C, G). You will be notified in the R console if the sequence contains invalid characters.

Also, you will not be able to add parts with duplicate names or sequences to anything on the list. If the whitespace-removed, fully capitalized version of a messy sequence you attempt to add to the parts list matches a DNA sequence already entered into it, you will be notified of this in the R console and of which part your new attempted entry is a duplicate of. You will also be notified if the name for the part you are trying to enter is a duplicate of a name already in the list. These features can also be used to check sequences against your DNA parts on the list to see if they match.

NEVER EDIT PARTSLIST.TXT USING A TEXT EDITOR. THIS MAY PREVENT YOU FROM SUBSEQUENTLY ADDING NEW PARTS TO THE LIST. SEE BELOW FOR HOW TO REMOVE PARTS.

NEVER EDIT PARTSLIST.TXT USING A TEXT EDITOR. THIS MAY PREVENT YOU FROM SUBSEQUENTLY ADDING NEW PARTS TO THE LIST. SEE BELOW FOR HOW TO REMOVE PARTS.

If your partslist.txt file contains only 1 entry, just delete the file.

If there is more than 1 entry in partslist.txt, to remove DNA parts from the parts list:

Open the VESICLES-master folder. Make sure the partslist.txt file that you want to remove parts from is in the folder. Double-click and open deleteLotsOfPartsFromList.R with RStudio. Run the script. In Rstudio, using the keyboard shortcut CTRL+ALT+R does this. Alternatively you can click through the menu bar.



Next, at the bottom of the R Console for as many parts as you want to delete, type: deleteLotsOfPartsFromList("part name 1", "part name 2", "part name 3",...). Please note the quotation marks must be included. Now hit enter:



The part names and their sequences will be removed from partslist.txt:



You will be notified in the R console window if the part was successfully deleted from the list or if your attempt to delete anything was unsuccessful.