StackThread Software Ltd., 2012

Diabetes+ is an iPhone application to help patients monitor and manage their diabetes. Specifically, the app allows patients to record their blood glucose, bodyweight, insulin doses, cholesterol, blood pressure, and carbohydrate and calorie intake.

The app also allows patients to keep track of their bodyweight, HbA1c and blood pressure targets, plot their data on a series of charts and export their data to major spreadsheet packages such as Microsoft Excel or Numbers from Apple's iWorks suite.

Diabetes+ can be downloaded from the App Store here.

MyTITL: MySQL Tree Insert From Tab-Indented List

Diabetes Trials, 2011

MySQL Tree Insert From Tab-Indented List (MyTITL) is a small PHP program that accelerates the process of importing hierarchical data into flat-file or relational databases. MyTITL will take a tab-indented list in plain text format and generate a SQL INSERT statement to create a table using what is variously described as the nested set model or modified preorder tree traversal.

Note that the nested set model is best suited to trees that are read-only and is especially well-suited for read-only use in databases that lack native support for recursive query constructs (such as MySQL). Inserting, moving or deleting nodes in a nested set is extremely expensive relative to, e.g. an adjacency list, as the nested set requires updates to a high percentage of entries in the left and right columns. Hence, MyTITL is basically designed to quickly import read-only hierarchical data structures into MySQL.

MyTITL is licensed under a Creative Commons Attribution 3.0 Unported License and can be downloaded from GitHub here.

Neuroanatomy Dictionary

Neuroanatomy Dictionary

StackThread Software Ltd., 2011

Neuroanatomy Dictionary is an iPhone application designed for medical students and professionals to learn and revise neuroanatomy terms and definitions. The content was meticulously prepared by Mr Jonathan Pesic-Smith and Mr Ciaran Scott Hill.

Terms can be rapidly located either through the alphabetical listing or by text search. Neuroanatomy Dictionary also allows entries to be marked as "favorites" for those terms whose definitions are frequently required or are proving difficult to commit to memory.

Neuroanatomy Dictionary can be downloaded from the App Store.


MRC Laboratory of Molecular Biology, 2007

BioSAVE (Biological Sequence and Annotation Viewer) is a piece of Mac OS X software for viewing annotations of DNA and protein sequences. The program was written in Objective C using Apple's Cocoa frameworks.

BioSAVE icon

BioSAVE natively reads sequence annotations in GFF format, but also supports script plug-ins to convert other annotation formats to GFF on-the-fly from the comfort of the open dialog box. Sequence data can be read in either plain text (for single sequences) or FASTA format.

If the annotation file contains statistical scorings, BioSAVE will present two sliders allowing upper and lower statistical cutoffs to be set; BioSAVE will dynamically show only those motifs which fall within the specified range. Even better, the motifs that do fall within the range are shaded dynamically to represent approximately where in the range they fall (darker shading can be set to represent either higher or lower scores).

BioSAVE in action

BioSAVE can also display an arbitrary number of additional annotation tracks along the length of the sequence (see screenshot, right). This allows additional data, such as ChIP enrichment or evolutionary conservation, to be quickly viewed in place. Since the tracks utilise the very same plug-in architecture as the main annotation, a script could easily be used to pull the track data live from the web, a MySQL database or the local file system.

BioSAVE can found, along with considerable supporting documentation and example data sets, on the Theoretical and Computational Biology group page at the MRC-LMB. It requires Mac OS X 10.3.9 and up.