SIMScells' underlying Methodology

SIMScells products and services are supported on a strong scientific basis, to offer researchers the highest quality and the most reliable results. On one hand, the Therapeutic Performance Mapping System® (TPMS®) Anaxomics proprietary technology is a cutting-edge bioinformatics technology applied to the construction of bio-pathological maps. On the other hand, the patented TPMS® technology is also a method of searching and hand-curating biological and clinical data to obtain highly comprehensive and accurate databases.

The list below contains a list of white papers explaining in simple language different aspects of the TPMS® methodology:

Protein fingerprints pave the way for microarray comparison

Journal: White Paper

Authors: Mulet R, Pujol A, Sardón T, Farrés J, Mas JM

Anaxomics has developed a novel method of analysis for microarray data based on the generation and subsequent comparison of 2D fingerprints for each sample. Microarray results are incorporated into a protein interaction network and embedded with all sorts of biological and medical data. Multidimensional scaling is use to reduce the multidimensional network into a 2D map, generating a specific projection "fingerprint". A repertory of cell-type specific 2D fingerprints based on previous experiments stored in GEO database has been generated. The cell-type fingerprints obtained can be envisaged as the average population. Thus, in addition to objectively quantifying the overall differences between samples, this revolutionary approach can measure the relative distance between any microarray sample and the cell type average.

Anaxomics' Methodologies. Understanding the Complexity of Biological Processes

Journal: White Paper

Authors: Valls R, Pujol A, Farrés J, Artigas L, Mas JM

Biological processes arise from nature's inherent complexity, and they involve many components connected with positive and negative feedback, sometimes with redundant circuitry, sometimes with differential pathways in different individuals, sometimes with blurry, and conditional and variable connectivity patterns.
In consequence, an intuitive understanding of their dynamics is hard to obtain. Anaxomics' proprietary TPMS technology consists of a compendium of cutting-edge computational tools to mathematically model any biological process. In this way, Anaxomics offers its broad expertise in Systems Biology and its state-of-the-art biocomputational methodologies to provide a new insight in the understanding of the complexity of biological processes. This document describes Anaxomics' methodologies to understand any biological process together with its intrinsic complexity.

Assessing drug target association from biological evidences

Journal: White Paper

Authors: Segú C, Farrés J, Artigas L, Mas JM

The full drug target profile identification is many times a necessary step in drug development process. Recently, the move to a more holistic approach in drug discovery has resulted in the increasing use of cell-based assays to discover new biologically active small molecules. The subsequent identification of the molecular targets that underlie an observed phenotypic response--termed target deconvolution--is an essential step.
This paper describes a method developed by Anaxomics for the prioritization of potential drug targets based on general biological knowledge, Systems Biology and drug-related biological and physiological data.