IT / Software / Bioinformatics

CellNetAnalyzer (CNA) is a MATLAB toolbox providing various computational methods for analyzing structure and function of metabolic, signaling, and regulatory networks. For metabolic networks, CNA supports a variety of stoichiometric and constraint-based modeling techniques, including flux balance analysis (FBA), metabolic flux analysis, elementary-modes analysis, or computational strain design (e.g., minimal cut set analysis). Signal transduction and (gene) regulatory networks can be ...

Engineering light distributions in a three-dimensional volume to achieve selective illumination profiles is an instrumental task shared by many optical and microscopy techniques. The optimization of the light distribution can lead to significant enhancement of relevant performance figures and ultimately to the extension of the instrument or experimental protocol capabilities^1,2,3,4,5. Targeted illumination profiles can be used either to mechanically interact with molecules at nanometer ...

Robots need detailed haptic sensing that covers their complex surfaces to learn effective behaviors in unstructured environments. However, state-of-the-art sensors tend to focus on improving precision and sensitivity, increasing texel density, or enlarging the sensed area rather than prioritizing system robustness and the usability of the sensed haptic information.

MARS is a powerful program for robust automatic backbone assignment of proteins. MARS is applicable to proteins with extreme chemical shift degeneracy such as high molecular weight proteins and partially disordered or fully intrinsically disordered proteins. MARS is successfully used in many labs world-wide as evidenced by a huge number of citations.

NMR spectroscopy is a unique technique for the assignment of the constitution, configuration and conformation of small molecules, natural products, proteins, nucleic acid and oligosaccharides. NMR-derived residual dipolar couplings overcome limitations associated with traditional NMR data, avoid data misinterpretation and provide novel insights into structure-activity relationships. In order to leverage the full potential of residual dipolar couplings, however, powerful dedicated software and ...

In the last decade, high-resolution computed tomography (CT) and microcomputed tomography (micro-CT) have been increasingly used in anthropological studies and as a complement to traditional histological techniques. This is due in large part to the ability of CT techniques to nondestructively extract three-dimensional representations of bone structures. Despite prior studies employing CT techniques, no completely reliable method of bone segmentation has been established.

SIMNRA is a Microsoft Windows program for the simulation of energy spectra for ion beam analysis with incident ions from about 100 keV to many MeV. SIMNRA can be used for the simulation of Rutherford backscattering (RBS), elastic backscattering with non-Rutherford cross-sections (EBS), nuclear reaction analysis (NRA), elastic recoil detection analysis (ERDA), and medium energy ion scattering (MEIS). Almost 3000 different non-Rutherford and nuclear reactions cross-sections for incident protons, ...