Software

RDrugTrajectory – R Package for the analysis of drug prescriptions in electronic healthcare records

An R package designed for the analysis of CPRD prescription electronic healthcare record (EHR) data.

R package can be downloaded from Github.

This R package came about as the result of supervising a very talented post-graduate Clinical Neuroscience student (please see Credits). The student’s project, titled “A Longitudinal Cohort Study of Migraine Preventative Medication Usage in UK CPRD” required immediate access to primary care clinical and prescription records of patients suffering with headache disorders. The CPRD data can be very overwhelming, especially to those with little experience in electronic healthcare records or the manipulation of large data sets. To mitigate this concern I decided to develop a drug-prescription themed R API. Whilst I was writing the R package my student was putting it to use, performing the analysis necessary to answer the research aims whilst reporting bugs and suggesting additional features. My ethos is to build an R package that can interrogate CPRD records whilst requiring minimal R language experience (although some experience goes a long way).

CPRD Additional Clinical record retrieval using R

R scripts and information concerning the retrieval of patient additional clinical data. Please note: this is a live project, with new R code and CPRD properties being added when possible.

R scripts can be downloaded from Github.

Please see the F1000 short-methods publication to learn more: 10.12688/f1000research.26228.1

A CPRD (Clinical Practice Research Datalink) data request will usually return a primary care clinic file(s) and corresponding additional clinic file(s). The clinic files hold the patient to GP consultation concerns (a medical diagnosis and/or complaint) along with anything prescribed by the GP and on the NHS (drugs, supports, special foods etc). Particular patient characteristics that may be of a medical concern are recorded by the GP into the additional clinic file and linked back into the clinic file by way of patid, adid and the enttype (event type). Using this link between the two tables, a series of look up files and the medcodes provided by CPRD, a researcher could, for example, decode the complete smoking history, BMI records, family history of a patient, and any blood works of patient.

IR and Raman spectroscopy visualisation using R

R code to visualise spectra from the ORCA output file.

R scripts can be downloaded from Github.

These R functions were just a little bit of fun to tie my experience of using R with an attempt at forever improving my understanding of theoretical biophysics and computational chemistry.

ChemInformatics – no longer supported

I’ve started an R wrapper project for a number of ChemInformatics and Transcriptional Drug response tools. This is a basic 5% project i.e., when I get the time, that allows the user to can preexisting ChemInformatics R packages in a logical and easy to follow manner. Please be patient whilst I work on this. The initial GitHub repo is going to be confusing, to say the least, until I find the time to structure the code and workflows/tutorials.

https://github.com/acnash/ChemInformatics

ForceGen

A large number of crystallographic protein structures include ligands, small molecules and post-translational modifications. Atomic bond force constants for computational atomistic models of post-translational or non-standard amino acids, metal binding active sites, small molecules and drug molecules are not readily available in most simulation software packages.

We present ForceGen, a Java tool that extracts the bond stretch and bond angle force constants and equilibrium constants from the Hessian of a Gaussian vibrational frequency analysis. The parameters are compatible with force fields derived using the second order tensor of the Hessian. The output is formatted with the Gromacs topology in mind.

The software and sample files can be located at the address: https://sourceforge.net/projects/forcegen/

A video tutorial is available here.

explosive

MARDy

MARDy is a curated database of known resistance mechanisms and associated antifungal drugs. There are four major classes of drugs for the treatment of fungal infections: polyenes, azoles, echinocandins, and antimetabolites. Antifungal drug resistance is a complex phenomenon involving multiple mechanisms. MARDy includes resistances as a product of amino acid substitutions, tandem repeat gene sequences, and chromosome ploidy.

The website can be accessed at the address www.mardy.net

DNA

Water removal from a bilayer core – script

This Perl script will remove water molecules from within the lipic bilayer chains between a defined Z coordinate per leaflet headgroup region (an approximation). I wrote this in the first year of my PhD, just over seven years ago. It is extremely useful when constructing new bilayer Molecular Dynamics system. The script has been designed for Gromacs and with water molecules defined as SOL and with an OW atom type present. Providing you’ve built your bilayer normal to the z-axis, after solvating your system you can determine the two z points between which water should be removed by visualising your system in VMD. Just remember, VMD uses angstroms and this script (Gromacs) requires nanometres, so on the command line change e.g 23 56 (VMD) to 2.3 5.6 (Gromacs), to define the start and end of the lipid chains in the z-axis.

Download the script from here (remove_water1_2.pl).