The purpose of this cloud lab is to investigate the phototactic behavior of Euglena gracilis remotely over the Internet without having to come to a wet lab.
Visit euglena.stanford.edu, create a user account, and log in. The first thing you will see is a dashboard with a list of available Biotic Processing Units (BPUs) that host cultures of Euglena in microfluidic chambers (Figure 1). We have two different types of microscope magnification that look into these chambers, 10x (“larger Euglena”) and 4x (“smaller Euglena”).
Let's click on the “Control any available microscope live” button, which might pop up a confirmation dialog once a BPU is available. If it does, please do not check the option “Prevent this page from creating additional dialogs”, or else you will not be able to join the live experimentation system in the future. Note that the popup may take up to ~5-6 seconds to appear even when the system says the wait time is 0. Otherwise it will appear when a BPU is available (keep an eye on the wait time).
All wait times shown on the website are best estimates and may not be extremely accurate. After clicking “Ok” on the confirmation dialog, the website will take you to a Live Experimentation session like Figure 2:
The main display is a microscope view of the microfluidic device, which has four LEDs on each of the four sides of the display. You can use the joystick interface to shine a combination of these LEDs, which is indicated by the yellow bars (with intensity value, in percentage, written on them) along the side of the main display. The smaller display on the bottom right corner is just a peek into our real hardware in action. Perhaps you can watch the real LEDs go off in real-time as you move your joystick, but a more interesting thing to watch would be how the Euglenas react to your joystick. A single live experimental session will last for 1 minute and you can run as many experiment sessions as you want.
You can also run live experiments on a specific BPU of your choice by clicking the “Live” button found above every BPU as shown in Figure 1. However, if everybody wants to use that specific BPU at the same time then there will be a long wait time!
All experimental data can be downloaded as a compressed file (tar.gz format) from the front page (see Figure 3). They are sorted so that the latest one is at the very top. If you are using Windows you may have to download some tool that can uncompress tar.gz (e.g, 7-Zip is a free option). The data basically comes with a movie file named “movie.mp4” with the corresponding light and timing information in a lightdata.json file (JSON format).
Once the experiment is done the data will appear on the front page as discussed above. Depending on the load on our system, it may take some time before your data is ready and you may need to refresh your front page to see the new data.
You can also program light values using a simple CSV file (Figure 4 that can be generated in Google Spreadsheets, copy and modify this file into your own google Spreadsheet and save as CSV file. (You can also use MS Excel, but please use the “Windows Comma Separated CSV” as opposed to other CSV options). The time column is in milliseconds. Each row specifies the light intensities (0-100) at a given time. This illumination will be held until the next command or the end of the experiment. There is no fixed duration for an experiment in this mode and it will only run until the last row! The items in red must be present. Make sure there is no extraneous spaces.
For example, in Figure 4, all the lights will be turned off at time 0 (the first thing in the experiment) until the 30th second when the top LED will be turned on with full brightness (100) and held until the 70th second, at which point the right LED is turned on to its full brightness. However, the command at the 70th second is the last one in the program, so the experiment will end immediately and all LEDs will be turned off. So, if you want to hold this light you will need to add a dummy row with all zeros at an appropriate time. You can utilize the “tag” row as an identifier which will appear in the “tag” column on the front page for easy navigation.
Browse and upload the CSV files to our system from the front page (you can choose multiple files at once – but we suggest you only submit one at a time) by clicking on the button “Batch” as shown in Figure 1 and then press “Submit pre-defined experiments to any available microscope” button. The system will route your experiments to BPUs with the least wait time. However, like the Live experimentation mode, if you like to run your experiments on a specific BPU, press the “Batch” button on top of the desired BPU. Note that this may not be optimal in terms of wait time.