Blog

The Blog is a collection of News, Blog posts, technical tips and tricks and other writings from my sphere of interest.
- Esben Jannik Bjerrum

Mar

In the NIR news (again)…..

Esben Jannik Bjerrum is in the (NIR) News again. This second part concludes the announcement of the Fulgur application, by introducing an overview of the source code as well as highlighting a way of working with Matlab GUI programming that takes the synchronization hassles out of it. The first part of the articles introduced the Fulgur program itself, which is ...

Feb

The chemoinformatics package Rdkit has is strength with handling small organic molecules. These molecules are characterized by a large diversity in chemical structures. A description of the exact way the atoms bond together are necessary to understand what molecule it is. Biological macro molecules are often build from repeating sequences of standard building blocks, such as amino-acids or ...

Feb

Feature selection is a powerful way of reducing the complexity of a machine learning or statistical model. But feature selection must be done in the right way, or you may end up cheating yourself or others. Later we will also see if green jelly beans are truly associated with acne. When working with machine learning, it may be a good idea ...

Feb

New Web Page

Wildcard Consulting has launched its new web site. The site has moved to a WordPress installation which has a lot more features and options than the previous CMS system. In the process the pages have been updated, and the previous info and blog posts have been moved to ...

Jan

Chaos in Excel, Deliberately!

Yes, I deliberately put Chaos in Excel! In form of a simulation of the logistic equation which shows non-linear behaviour for certain values of the feedback constant;-) The Excel workbook is available for download and make it possible to play around with the feedback constant and hopefully get a better understanding of non-linear behaviour a.k.a. Chaos. Have fun ;-) The Logistic ...

Jan

Death from Swapping

Can Python be used for machine learning with 1.400.000 samples on a regular desktop PC? The Python programming language showed its worth for rapid model development in a machine learning open innovation challenge. However, it meets its limit when the model and the data set cannot fit in the computers main memory at the ...

Jan

Welcome Nele Plutus as Marketing Intern

Today Nele Plutus will start her 4-week internship at Wildcard Pharmaceutical Consulting. In this period she will work as a marketing intern with developing a plan and strategy for Wildcard Pharmaceutical Consulting's online presence and homepage. 

Jan

Last time a simple multiple linear regression (MLR) model was seriously overfitted to molecular solubility data. This time the concept of regularization will be tested. Recall that the MLR model was of the form: y = b1*x1 + b2*x2 + … + bi*xi + b0 Where each x correspond to the absence or presence of a particular bit in the morgan fingerprint and ...

Jan

Wildcard has renewed its coorporate membership with the Danish red cross for 2016 and thus supports their humanitarian work. The Red Cross movement builds on seven principles: Humanity The International Red Cross and Red Crescent Movement, born of a desire to bring assistance without discrimination to the wounded on the battlefield, endeavours, in its international and national ...

Dec

Last blog entry the conversion between molecule and fingerprint was briefly touched upon. Now the fingerprints will be used as the basis for a simple attempt to build a solubility model using some data from the web. The file with some 1000 molecules as smiles and their aqueous solubility was downloaded fromhttp://www.vcclab.org/lab/alogps/

Nov

The headline is a bit misleading as it's not fingerprints of criminals, but chemical fingerprints. Chemical fingerprinting is a way of converting drawn molecules into streams of bits, 0 and 1's. An old fingerprint type are the MACCS keys, which was developed by former MDL as a fast way of do substructure screening in molecular databases. The public version comprises ...

Oct

Rdkit is a nice cheminformatics toolkit with python bindings. Wildcard Pharmaceutical Consulting have over the years used it a lot for a couple of different projects in Python Programming. However, RDKit strives to ensure that the molecules created makes chemical sense, which can be a show stopper when working with large ...

Oct

New Office Space

From 1st september Wildcard Pharmaceutical Consulting will get a new office space at Copenhagen Bio Science Park Cobis.dk.   Wildcard Pharmaceutical Consulting Copenhagen BioScience Park Ole Maaløes Vej 3 DK-2200 Copenhagen N

May

Molecular mechanics treats molecules as ball and spring systems using classical mechanical physics. Molecules are modeled as ”balls on springs”, and the total conformational energy are described as a sum of spring constants, torsional terms, vdWalls interaction, Couloumbic interactions etc. This collection of terms are known as a force field, and enables fast conformational ...

Oct

This example shows how to create a simple graphical user interface (GUI), using GUIDE and a Model-Controller-Viewer like organization (Figure 1). The example draws on the Simple GUI tutorial from the Mathworks documentation: http://www.mathworks.se/help/matlab/creating_guis/about-the-simple-guide-gui-example.html If unfamiliar with Guide and GUI developement, follow that tutorial first. The structure of the program is however ...