Computational Medicine

Lipido

The so-called Friedewald formula for LDL cholesterol has been at the heart of cardiovascular risk assessment since the 70's, but recently the scientific community has focused on the finer structure of lipoprotein particles. Lipido is an epidemiologically validated software to extract more detailed information from the basic lipids (triglycerides, total and HDL cholesterol), without any new biochemical measurements

Cholesterol-carrying lipoprotein particles in blood have long been recognized as key contributors to the development of vascular disease and subsequent incidence of heart attack or stroke. Due to technical difficulties, the information available in clinical practice has been limited to total cholesterol concentration, cholesterol content of high-density lipoproteins (HDL-C) and total concentration of triglycerides. For this reason, a mathematical formula (by Friedewald et al.) for the biologically interesting low-density lipoprotein (LDL-C) was derived from the three basic quantities already in the seventies.

Strictly speaking, the Friedewald formula does not estimate pure LDL-C concentration, but the sum of intermediate density lipoproteins (IDL-C) and LDL-C, with small amount of Lp(a). Lipido is a software that aims to extend the rationale of Friedewald to other important lipid and lipoprotein markers such as triglycerides in very low-density liporoteins (VLDL-TG) and apolipoproteins. The software also calculates estimates for pure LDL-C and IDL-C, thus improving the specificity of the Friedewald formula.

This work spawned from a collaborative project between a number of Finnish study groups. The Computational Medicine Research Group (formely within Helsinki University of Technology, now affiliated with University of Oulu) created the neural network models from an extensive training set of lipid measurements. The results were then validated in the FinnDiane set of type 1 diabetic patients. The computational models involved are complicated; we have therefore created an easy-to-use online interface, which should provide adequate service to all interested.

J. Niemi, V.-P. Mäkinen, J. Heikkonen, L. Tenkanen, Y. Hiltunen, M. L. Hannuksela, M. Jauhiainen, C. Forsblom, M.-R. Taskinen, Y. A. Kesäniemi, M. Savolainen, K. Kaski, P.-H. Groop, P. T. Kovanen, M. Ala-Korpela Estimation of VLDL, IDL, LDL, HDL2, apoA-I and apoB from the Friedewald inputs – apoB and IDL, but not LDL, are associated with mortality in type 1 diabetes Annals of Medicine 41, 451-461, 2009

See the online version >>

MeliKerion

The self-organizing map is a popular data mining tool, but so far it has not been fully applied outside engineering sciences. MeliKerion is an open source package for SOM analyses in the Octave/Matlab programming environments, but you can also take advantage of the multi-dimensional visualization via the online service.

CraneFoot

CraneFoot is an open-source pedigree drawing software that can process hundreds of families simultaneously and print a comprehensive report of the results. An online drawing service is provided for those that do not wish to use the software without a graphical user interface.

Himmeli

Drawing complex networks is no trivial matter especially if they are weighted, and for this reason an automated solution was created. Himmeli is built on a simulated annealing algorithm that spreads the nodes in two dimensions for best viewing on printed media.

Miscellaneous tools

Managing and preprocessing datasets is crucial for efficient and accurate statistical modelling. Most of the tasks are repetitive and general in nature, and as such good targets for automation. The software tools in this site are designed primarily for the FinnDiane study group, but may be of use to other researchers as well.

More information

Mika Ala-Korpela, PhD
Professor in Computational Medicine

University of Oulu & Biocenter Oulu
Faculty of Medicine
Institute of Clinical Medicine
FI-90014 University of Oulu
Finland

Mobile: +358 40 1977 657
E-mail: