Description of the Software. Subject to the terms and conditions of this XXXX, you can download, or attempt to download, the Software on your PC; provided, however, that the Software will only function properly where your PC utilizes a Microsoft Windows operating system. If you experience any problems installing and/or uninstalling the Software, please contact us via e-mail at: xxxxxxx@xxxxxxxxxxx.xxx.xx.
Description of the Software. The "PUBLISHER" has designed and developed 13CFLUX2 which consists of a set of applications for performing 13C‐based Metabolic Flux Analysis (13C‐MFA), i.e. the simulation‐based estimation of in‐ vivo metabolic reaction rates. In particular, the implemented type of 13C‐MFA relies on 13C labeling measurement data obtained from an organism which is kept under metabolic and isotopic stationary conditions. The 13C labeling measurement data are usually (but not necessarily) generated using mass spectrometry (MS) or nuclear magnetic resonance (NMR) measurement devices. The estimation of in‐vivo reaction rates for very large metabolic networks, the evaluation of a series of high throughput experiments, as well as the evaluation of nonlinear statistics and experimental design involves a high computational effort. By implementing newly developed simulation algorithms, which are highly tuned for the underlying mathematical problems, using 13CFLUX2 allows to perform 13C‐MFA studies on a common desktop computer. Network models and measurements are authored in the FluxML document format. Unique characteristics of the 13CFLUX2 software suite are: • significantly improved performance and higher numerical accuracy compared to the predecessor version 13CFLUX and other available software packages for 13C‐MFA; • professional input and output via XML‐based file formats and HDF5 (hierarchical data format, version 5); • a comprehensive error handling including comprehensible error messages; • statistical analysis of the obtained reaction rate distribution and tools for performing optimal experimental design; • support for multi‐core CPUs and computer clusters. The following license terms apply to the software's executable files as well as to the included manuals and data files (in this agreement referred to as the "SOFTWARE"). Likewise, these terms apply to any 13CFLUX2 software update provided by Forschungszentrum Jülich GmbH, unless separate license terms accompany those items. If so, those license terms apply. BY INSTALLING AND/ OR USING THE SOFTWARE, YOU ACCEPT THE TERMS OF THIS LICENSE AGREEMENT. IF YOU DO NOT ACCEPT IT, DO NOT INSTALL AND USE THE SOFTWARE. IF YOU COMPLY WITH THESE LICENSE TERMS, YOU HAVE THE RIGHTS AS SPECIFIED BELOW.
Description of the Software. Prime/STUDIO is a packet of applications for the programming and management of INIM designed Prime intrusion control panels. The software manages connections with control panels via USB, TCP/IP, GPRS or GSM and therefore allows remote maintenance via the Internet. The Prime/STUDIO graphic interface allows operators to interact directly with the control panel, identify wiring faults, update the configurations of connected devices, change device addresses and view function parameters. The software also provides system monitoring functions that allow real-time viewing of the statuses of the loop devices, zones and timers, etc. All of this is achieved through the command functions. These functions allow the operator to work on the monitored systems via map icons which represent the system objects, or by means of preset buttons defined during the configuration phase.
Description of the Software. The LMPCA software program is a MATLAB graphical user interface for fitting the linked- mode PARAFAC-PCA model (Wilderjans et al., 2009) to a coupled data set consisting of a real-valued three-way data array and a real-valued two-way data matrix that have one mode in common. Given such a coupled data set, the LMPCA software program estimates a user- specified range of linked-mode PARAFAC-PCA solutions with increasing complexities (i.e., number of components) by making use of a multistart alternating least squares algorithm. In order to help the user in determining the number of components that are present in the data, a scree plot and fit information for all complexities considered, are displayed in the output files that are created by the LMPCA program. For more information about how to handle the LMPCA software program, see Wilderjans, Ceulemans, Kiers, & Xxxxx (2009).
Description of the Software. The MultiBlock Component Analysis (MBCA) software allows to fit a set of component models to multivariate multiblock data (e.g., observations from a set of variables for subjects that are embedded in groups). Given such multivariate multiblock data, the MBCA program performs separate principal component analyses on all data blocks, simultaneous component analyses and/or clusterwise component analyses with increasing complexities (i.e., number of components and, in the latter case, number of clusters) by means of a multi-start alternating least squares algorithm. Missing data are imputed through weighted least squares fitting. In order to help the user in determining the number of components and/or clusters that are present in the data, the results of a model selection procedure are displayed in the output files of the MBCA program. The MBCA program is available in MATLAB and as a standalone (".exe") application. More information about how to handle the MBCA software can be found in De Roover, Ceulemans & Xxxxxxxxx (2011).
Description of the Software. The GAME is proprietary software that is owned and developed exclusively by SAAV Games. The maximum number of tokens implemented in the software is 1,000,000,000. The software does not permit change to the number of implemented tokens after the smart contract is deployed on the Network.
Description of the Software. The detection of cis-regulatory modules (CRMs) that mediate transcriptional responses in eukaryotes remains a key challenge in the postgenomic era. A CRM is characterized by a set of co-occurring transcription factor binding sites (TFBS). In silico methods have been developed to search for CRMs by determining the combination of TFBS that are statistically overrepresented in a certain geneset. Most of these methods solve this combinatorial problem by relying on computational intensive optimization methods. As a result their usage is limited to finding CRMs in small datasets (containing a few genes only) and using binding sites for a restricted number of transcription factors (TFs) out of which the optimal module will be selected. ModuleDigger is a tool based on an itemset mining based strategy for computationally detecting cis-regulatory modules (CRMs) in a set of genes. ModuleDigger can handle larger dataset as well as considering a genome-wide view which means it is considered specific for the whole cluster of input genes if the CRM is statistically more overrepresented in this cluster of genes than in the remainder of the genome. By exploiting the computational efficiency of an itemset mining approach and combining it with a well-designed statistical scoring scheme, we were able to prioritize the biologically valid CRMs in a large set of coregulated genes using binding sites for a large number of potential TFs as input.
Description of the Software. ViTRaM is a tool that is capable of visualizing overlapping transcriptional modules in a very intuitive way. ViTraM allows for a dynamic visualization of overlapping transcriptional modules in a 2D gene-experiment matrix. Multiple methods are included for obtaining the optimal layout of the overlapping modules. features: -In addition to the previously developed tools for visualizing multiple modules, ViTraM also allows to display additional information on the regulatory program of the modules. The regulatory program consists of the transcription factors and their corresponding motifs. -A first way of obtaining information on the regulatory program is by using the information from curated databases. This information can be used to further analyze modules inferred by biclustering algorithms. -Secondly, information on the regulatory program can also be the outcome of a module inference tool itself. Both types of information on the regulatory program can be included by ViTraM. -By visualizing not only the modules but also the regulatory program, ViTraM can provide more insight into the modules and makes the biological interpretation of the identified modules less complicated for biologists.
Description of the Software. The nonnegative real-valued model of hierarchical classes (NNRV-HICLAS) software allows to fit nonnegative real-valued hierarchical classes models to two-way two-mode data (e.g., a rectangular objects by attributes data matrix). Given such data, the NNRV-HICLAS program performs nonnegative real-valued hierarchical classes analyses of a prespecified complexity (i.e., number of object and attribute clusters) by means of a multi-start two-stage algorithm combining a simulated annealing and an alternating local descent stage. The NNRV-HICLAS program is available in MATLAB.
Description of the Software. The Diffusion Model Analysis Toolbox (DMAT) is a collection of MATLAB files that implement an algorithm for quickly and efficiently estimating the parameters of the Xxxxxxxx Diffusion Model. Details of the model and the algorithm are provided in Vandekerckhove and Tuerlinckx (2006). DMAT also contains extra tools, such as a graphical user interface (GUI), a rescue tool, documentation, demonstrations and more.
