Informatics

Chemical Structures in Databases (blog article 7 of 8) : Under The Bonnet

As the SQL feature set doesn't provide for chemical structures to be queried directly as shown below, the chemical moiety must first be ...Read more

Chemical Structures in Databases (blog article 6 of 8) : Chemical Awareness

One of the many roles of IUPAC has been to establish and maintain systematic rules for the nomenclature of chemical entities. Within the ...Read more

Chemical Structures in Databases (blog article 5 of 8) : Subgraph Isomorphism

A mathematician might define subgraph isomorphism as the determination of a subgraph of a graph which is isomorphic to another graph. From the chemo-informatic ...Read more

Informatics RDBMS storage and manipulation of chemical moieties (blog article 4 of 8)

Over the past three decades, COTS products from major chemoinformatics solution providers have offered a number of technologies for the storage and manipulation ...Read more

Chemical Structures in Databases (blog article 3 of 8) : Extensible Indexing

Traditionally database indexes, a mechanism to quickly locate data within the database without significant performance penalty, have been limited to database data type primitives. ...Read more

Chemical Structures in Databases (blog article 2 of 8) : Chemical Structure Databases

The Cope-Chat approach previously described remains the crux of most chemoinformatic database systems. The implementation provides a mechanism to search on chemical (sub)structure or reaction scheme ...Read more

Chemical Structures in Databases (blog article 1 of 8) : Cope-Chat cards, some 1930’s technology

A most fascinating and simple early technology for the indexing of information, a precursor to databases and their respective indexes, used Cope-Chat (Copeland ...Read more

MongoDB as a DNA Typing Database (SGMPlus?)

Is MongoDB up to the job of being able to query a database of ca. 10,000,000 SGM Plus DNA profiles and laboratory samples? ...Read more

The struggle of Software Requirements: Mass Spectrometry EIC Peak Aggregation vs. Time

Software developers have to endure many recurring frustrations. One of my pet hates is having to trawl through software requirement documents bloated out with ...Read more

CODA: A Noise and Background Reduction Method for Component Detection in Liquid Chromatography/Mass Spectrometry

The CODA algorithm has widespread use in the detection of 'real' peaks from noisy MS chromatograms. For example ACD Labs ChromManager and OpenChrom both cite CODA ...Read more