Search results for "computer interface"
showing 10 items of 189 documents
Protein knot server: detection of knots in protein structures
2007
KNOTS (http://knots.mit.edu) is a web server that detects knots in protein structures. Several protein structures have been reported to contain intricate knots. The physiological role of knots and their effect on folding and evolution is an area of active research. The user submits a PDB id or uploads a 3D protein structure in PDB or mmCIF format. The current implementation of the server uses the Alexander polynomial to detect knots. The results of the analysis that are presented to the user are the location of the knot in the structure, the type of the knot and an interactive visualization of the knot. The results can also be downloaded and viewed offline. The server also maintains a regul…
SymbioGenomesDB: a database for the integration and access to knowledge on host-symbiont relationships.
2014
Symbiotic relationships occur naturally throughout the tree of life, either in a commensal, mutualistic or pathogenic manner. The genomes of multiple organisms involved in symbiosis are rapidly being sequenced and becoming available, especially those from the microbial world. Currently, there are numerous databases that offer information on specific organisms or models, but none offer a global understanding on relationships between organisms, their interactions and capabilities within their niche, as well as their role as part of a system, in this case, their role in symbiosis. We have developed the SymbioGenomesDB as a community database resource for laboratories which intend to investigat…
GYROCOMPU: Toolbox Designed for the Analysis of Gyrotron Resonators
2020
The key point of gyrotron design is the analysis of the radio frequency (RF) behavior in gyrotron resonators. This article proposes a comprehensive, user-friendly and effective gyrotron design toolbox (GYROCOMPU) based on the MATLAB platform. GYROCOMPU associates a relatively complete set of codes for gyrotron analysis and integrates them together into a graphical user interface (GUI). The solving algorithm of the cold cavity equations and self-consistent equations is improved. The solving method improvement in these calculation algorithms renders the analysis more efficient and accurate. Three typical examples of gyrotrons working in the 140-GHz TE03 mode, 42-GHz TE03 mode, and 140-GHz TE1…
Dynamic interface for machine vision systems
2002
Iconic programming intends to provide expressive tools to implement, to debug, and to execute programs. For this purpose, visual languages need pictorial constructs and metaphors to guide the design of algorithms in interactive fashion. In the paper a new class of dynamic visual interfaces, named DIVA (Dynamic Interface for Visual Applications), is introduced, its properties are described, and an application to visual compilers in a multi-processors system dedicated to image analysis is given. Moreover, a formal definition of dynamic icon (DI) is also given.
Getting Docking into Shape Using Negative Image-Based Rescoring
2019
The failure of default scoring functions to ensure virtual screening enrichment is a persistent problem for the molecular docking algorithms used in the structure-based drug discovery. To remedy this problem, elaborate rescoring and post-processing schemes have been developed with a varying degree of success, specificity, and cost. The negative imagebased rescoring (R-NiB) has been shown to improve the flexible docking performance markedly with a variety of drug targets.The yield improvement is achieved by comparing the alternative docking poses against the negative image of the target protein’s ligand-binding cavity. In other words, the shape and electrostatics of the binding pocket is dir…
CandidaDB: a genome database for Candida albicans pathogenomics.
2004
CandidaDB is accessible at http://genolist.pasteur.fr/CandidaDB.; International audience; CandidaDB is a database dedicated to the genome of the most prevalent systemic fungal pathogen of humans, Candida albicans. CandidaDB is based on an annotation of the Stanford Genome Technology Center C.albicans genome sequence data by the European Galar Fungail Consortium. CandidaDB Release 2.0 (June 2004) contains information pertaining to Assembly 19 of the genome of C.albicans strain SC5314. The current release contains 6244 annotated entries corresponding to 130 tRNA genes and 5917 protein-coding genes. For these, it provides tentative functional assignments along with numerous pre-run analyses th…
Automated anaesthesia record systems, observations on future trends of development.
1995
The introduction of electronic anaesthesia documentation systems was attempted as early as in 1979, although their efficient application has become reality only in the past few years. Today, documentation technology is offered by most of the monitor manufacturers and new systems are being developed by various working groups. The advantages of the electronic protocol are apparent: Continuous high quality documentation, comparability of data due to the availability of a anaesthesia data bank, reduction of the workload of the anaesthesia staff and availability of new additional information. Disadvantages of the electronic protocol have also been discussed. Typically, by going through the proce…
DiseaseLinc: Disease Enrichment Analysis of Sets of Differentially Expressed LincRNAs
2021
Long intergenic non-coding RNAs (LincRNAs) are long RNAs that do not encode proteins. Functional evidence is lacking for most of them. Their biogenesis is not well-known, but it is thought that many lincRNAs originate from genomic duplication of coding material, resulting in pseudogenes, gene copies that lose their original function and can accumulate mutations. While most pseudogenes eventually stop producing a transcript and become erased by mutations, many of these pseudogene-based lincRNAs keep similarity to the parental gene from which they originated, possibly for functional reasons. For example, they can act as decoys for miRNAs targeting the parental gene. Enrichment analysis of fun…
German Registry for Acute Aortic Dissection Type A (GERAADA)--new software design, parameters and their definitions.
2011
BACKGROUND The working group for aortic surgery and interventional vascular surgery of the German Society for Thoracic and Cardiovascular Surgery (GSTCVS) initiated the web-based German Registry for Acute Aortic Dissection type A (GERAADA). It is the project's aim to collect standardized data from a large pool of patients with acute aortic dissections type A (AADA) to gain a deeper insight and knowledge to improve surgical therapies and perioperative management for these patients in the future. METHODS In addition to new medical insights, the working group has gained more experience over the last 4 years in how to collect valid and high-quality data. This experience led us to revise the dat…
Strategies for annotation and curation of translational databases: the eTUMOUR project
2012
Altres ajuts: LSHC/CT2004-503094 The eTUMOUR (eT) multi-centre project gathered in vivo and ex vivo magnetic resonance (MR) data, as well as transcriptomic and clinical information from brain tumour patients, with the purpose of improving the diagnostic and prognostic evaluation of future patients. In order to carry this out, among other work, a database-the eTDB-was developed. In addition to complex permission rules and software and management quality control (QC), it was necessary to develop anonymization, processing and data visualization tools for the data uploaded. It was also necessary to develop sophisticated curation strategies that involved on one hand, dedicated fields for QC-gene…