Geeky Stuff that makes C3 cool

Software tools


This python tool (written by Nick Rosa) enables us to keep track of our library of chemical stock solutions. When stocks are made they are scanned into the software and when they are finished they are scanned out. Simple as this concept is, it allows us to know what stocks we currently have, where they are, when they were made, and how often, on average, it takes us to use up 50 mL of the stock. Below is the entry for ammonium sulfate, our second most popular stock (PEG 3350 is our most popular).


This tool (written by Marko Ristic) builds on earlier work where we used a colour image to estimate the pH of a solution.  We now use a spectrophotometer to find the hue of a dyed solution, which is then translated into a pH value using a standard curve.  Every block of conditions (i.e. screen) we make up gets put through a pHUEristic analysis, to estimate the pH of each condition, which is then compared both to the pH of any buffer component in the solution and to any earlier records of the same block. pH values that vary by more than one pH unit from either the buffer pH or from the average pH of earlier records of the same condition in the same screen are flagged. The pH information can be found in the C6 report “Single screen contents”: it is located in the last column of the report (you may need to use the slider bars to see it).


This tool was the work of many people, most recently Chris Watkins. iQC (image Quality Control) takes the first inspection of each plate, finds the drop in each subwell, then finds the average displacement from the centre of the well, as well as the average lack of circularity. Small drops (<85% of the average area) are flagged, as are bubbles and splatter. A set of empirical standards are used to decide if the drops are perfect, excellent, good, fair or poor, within 2 hours of the plate being imaged. Plates with poor or fair results result in an email alert being sent to each C3 team member, so that the problem can be investigated.


Buffer pH Calculations

We use either the Henderson–Hasselbalch equation or an experimentally measured pH curve to estimate pH values obtained by mixing two end point stocks together. This is very convenient, as any pH between the pH limits of the two stocks can be accessed, using only two stocks.  The same HH calculations and the pH curves are also found in a spreadsheet.

Current Buffer_sheet


This is a python based application (initiated by Allen Gu) that allows us to track the contents of our -80 Freezer. Currently under development, we hope to tame the chaos which is the natural state of all laboratory freezers.