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All Topics > Biocomputational Focus > Visualization |
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9 projects in result set.
Whole-Cell Computational Model of Mycoplasma genitalium
- The goal of this project was to develop the first detailed, "whole-cell" computational model of the entire life cycle of living organism, <i>Mycoplasma genitalium</i>. The model describes the dynamics of every molecule over the entire life cycle and accounts for the specific function of every annotated gene product.
We anticipate that whole-cell models will be critical for synthetic biology and personalized medicine. Please see the project website <a href="http://wholecell.org">wholecell.org</a> and the Downloads page to explore the whole-cell knowledge base and simulations and obtain the model code. | |
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Registered: 2012-01-24 03:21 |
Practical Annotation and Exchange of Virtual Anatomy
- Representation of anatomy in a virtual form is at the heart of clinical decision making, biomedical research, and medical training. Virtual anatomy is not limited to description of geometry but also requires appropriate and efficient labeling of regions - to define spatial relationships and interactions between anatomical objects; effective strategies for pointwise operations - to define local properties, biological or otherwise; and support for diverse data formats and standards - to facilitate exchange between clinicians, scientists, engineers, and the general public. Development of aeva, a free and open source software package (library, user interfaces, extensions) capable of automated and interactive operations for virtual anatomy annotation and exchange, is in response to these currently unmet requirements. This site serves for aeva outreach, including dissemination the software and use cases. The use cases drive design and testing of aeva features and demonstrate various workflows that rely on virtual anatomy.
aeva downloads:
Downloads (https://simtk.org/frs/?group_id=1767)
Kitware data repository (https://data.kitware.com/#folder/5e7a4690af2e2eed356a17f2)
aeva documentation:
Guides and tutorials (https://aeva.readthedocs.io)
aeva videos:
Short instructions (https://www.youtube.com/channel/UCubfUe40LXvBs86UyKci0Fw)
aeva source code:
Kitware source code repository (https://gitlab.kitware.com/aeva)
aeva forum:
Forums (https://simtk.org/plugins/phpBB/indexPhpbb.php?group_id=1767 ) | |
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Registered: 2019-08-28 01:27 |
MITK-GEM: Software pipeline to GEnerate Models from images
- An attempt to provide a software pipeline to interactively create finite element models from medical images. Primarily intended to model bone fracture risk.
An application with graphical user interface and image processing plugins is provided. The application is build using the MITK Workbench software framework. The following plugins are available: fast image segmentation using graph cut, volume meshing using tetgen and density to modulus conversion for bone material property assignment.
Documentation and tutorials are available on our <a href="http://araex.github.io/mitk-gem-site/">tutorial website</a>.
Along with pre-compiled executables available here, the source code is available on our <a href="https://github.com/araex/mitk-gem">github page</a>.
The graph cut segmentation plugin and the material mapping plugin were developed as part of research studies.
If you use the software or source code in your research, please cite the corresponding journal <a href="https://simtk.org/project/xml/publications.xml/?group_id=1063">publications</a>. | |
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Registered: 2015-12-23 02:46 |
Live Cell NF-κB
- This project provides data and visualization tools to explore single-cell NF-κB dynamics. To view the interactive figure, please see the Downloads section. | |
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Activity Percentile: 55.30 Registered: 2013-03-05 01:40 |
ProDy: Protein Dynamics Analysis in Python
- ProDy is a free and open-source Python package for analyzing protein structural dynamics. It is designed and developed by Ahmet Bakan in Bahar lab at the University of Pittsburgh. New functional features are continually being added to ProDy. The following are the main features that have been successfully implemented to date:
The following are the main features that have been successfully implemented to date:
* Examination and analysis of structural variability observed in experiments:
- Efficient parsing of PDB files
- Powerful atoms selections and contact identification
- Matching, superposing, and comparing multiple structures/chains
- Principal component analysis (PCA) of X-ray structures
- PCA of NMR models
- PCA of mixed structural datasets from Blast search
* Prediction and analysis of protein dynamics using theory and simulation:
- Normal Mode Analysis using the Anisotropic network models (ANM)
- Gaussian network models (GNM) analysis
- Essential dynamics analysis (EDA) of MD snapshots
- Comparative analysis and visualization of dynamics | |
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Registered: 2010-12-28 19:53 |
FEATURE-Viz: A Web-Based Visualization System for Comparing
Pocket Similarity
- The PocketFEATURE algorithm seeks similar microenvironments within two binding sites, and assesses overall binding site similarity by the presence of multiple shared microenvironments.
Both the original perl implementation (http://simtk.org/home/pocketfeature) and the newer python implementation (http://simtk.org/home/pocketfeature2) produce text-based alignment results, with some small differences between implementations. FEATURE-Viz provides a web-based interface to visualize and manipulate alignments. | |
Activity Percentile: 0.00 Registered: 2015-04-15 19:50 |
Neurogene: Elucidating apoptotic pathways in brain tumor models
- Genomics has brought many important discoveries and changes into science and medicine. The central dogma of molecular biology where "DNA makes RNA and RNA makes protein" is well established (yet controversial). Watson and Crick had originally proposed a double stranded model of DNA. This served as a useful foundation for further understanding and research. Throughout the years more investigations demonstrated that human evolution was far more complex than originally believed. There was originally a great deal of migration around the world causing some hereditary lineages to become isolated and others to become more robust.
The life cycle of a cell usually begins with division and continues with replication. However, errors in mitosis can cause a cell to undergo apoptosis or form into a tumor. Differentiating between the two final pathways may be critical in helping to guide cells towards a less destructive pathway for the host organism. The critical component has to do with the environment the cell is in. The cell receives information from the outside environment and adapts according to received stimuli.
This project has been conceived to leverage a team based approach for elucidating the underlying apoptotic pathways responsible for tumor lysis and cell death. Combining the current understanding of molecular dynamics, genomics, and contrast imaging agents to discover novel therapeutic targets and further the current understanding of tumor biology within the genomic era. | |
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Registered: 2010-03-17 09:26 |
NetworkPainter: Biological pathway animation
- NetworkPainter is a web-based program for drawing and painting signaling network diagrams with high-dimensional cytometry data. Two versions of NetworkPainter are available. The <a href="http://covert.stanford.edu/networkpainter">NetworkPainter stand-alone version</a> is capable of visualizing any uploaded cytometry data. NetworkPainter is also available through the <a href="http://www.cytobank.org/networkpainter.html">Cytobank</a> flow cytometry repository. This version is capable of analyzing flow and mass cytometry data stored in Cytobank. | |
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Registered: 2014-01-10 00:11 |
Computational Analysis of Kinase Selectivity using Structural Knowledge
- Here, we present a knowledge-based approach to profile kinase selectivity based on the similarity between drug binding microenvironments. To allow large-scale kinase site similarity profiling, we have created a kinome structure database consisting of 5000 inhibitor-binding pockets from 187 unique human kinase crystal structures. | |
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Registered: 2017-04-18 20:03 |