Protocols, Code, and Interim Reports


[Handle Methods] This protocol describes, in detail, how to synthesize RNA/DNA hybrid handles and how to anneal them to RNAs etc. The protocol also describes how to crosslink antibodies to polystyrene beads, should you want to make your own. Most people simply buy streptavidin or protein G functionalized beads from Spherotech or Bangs Labs, though. If you are interested in this area, have a look at a paper from Nynke Dekker's lab - they did a very careful study of RNA annealing and DNA handle design. They found that simpler annealing buffers and temperature ramps work just as our original (more elaborate) 2001 protocol.

[MedianCI.nb] Mathematica function for calculating the confidence interval of the median. You provide a vector and the desired confidence interval, e.g. MedianCI[data, 0.05] to get the 95% CI. Mathematica's inbuilt MeanCI[data] provides the CI of the mean, but for data with outliers and/or lack of normality, the median is usually more suitable. This Mathematica function was directly translated from the one for R published at David-olives-median-confidence-interval.html.

[LogRank.nb] Mathematica function for calculating the Log-Rank statistic for two Kaplan-Meier curves. Given event times and censoring information for two groups (e.g. treatment and control), gives the Chi-Squared, Log-Rank, Z, SE, and p-value. LogRank uses Mathematica 8's SurvivalDistribution[data] and related censoring and plotting functions. The code is based on Giuseppe Cardillo's excellent logrank code for MatLab (22317-logrank), but the p-value is not Yates' corrected. Update: As of Mathematica 9.0, this functionality is now integrated in the kernel.

[MATLAB script] This MATLAB script can be used to quantify the fluorescence of cell nuclei in NPC transport studies.

[Octopus microscope control software] This is the GitHub repository for our microscope control software. We cannot provide support for this software. It is only available for Windows, but since it is written in C++, it should be relatively easy to port it to any other language and/or wrap it as needed (e.g. for use via Python). Please note that the code requires many external libraries and drivers which are provided by the hardware manufacturers and which we cannot redistribute to you. You will need to obtain these drivers and libraries directly from Andor, Olympus, Sutter, Physik Instrumente, Thorlabs, and National Instruments. What this means is that the package will not compile and it will not run, due to missing .h files and .dll files which are provided by the hardware vendors. By downloading the software, you agree that we are not liable for anything you do with it. Obviously, do not use this software to (try to) control your mars lander, pacemaker, or aircraft fly by wire system! There are much more professional software solutions available, especially Micro-Manager, but several of us here have our codebase memorized, making it very fast to fix problems or add new capabilities. If you are starting from scratch, you will almost certainly want to use Micro-Manager instead.

[Octopus file format] This is a short intro to the file format used by Octopus. Basically, you are dealing with a raw binary dump of everything that is coming from the Andor iXon camera. The files can be opened in all programming languages and many other programs, including imageJ, Fiji, Matlab, and Mathematica. See the .pdf for more info.