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Expert Systems Biology |
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The BioAnalytics Group LLC |
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Contact: |
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Phone: 609-632-0091 Fax: 609-632-1224 E-mail: info@bioanalyticsgroup.com |
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BioPathwise Features |
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BioPathwise2.0 is the only available system that is full-featured in both the simulation/drawing and data repository areas. The system’s intuitive tools support complex pathway-centric research with useful capabilities such as the ability to attached and store files along with pathways. Protocols for adding proprietary information to our database of public information, displaying and inputting kinetic information, de novo building of investigational pathways, and quality documentation throughout make for a positive and efficient user experience. To help you decide about ways that the BioPathwise 2.0 system can help your collaborations work more effectively, we’ve provided a features overview to highlight many of its significant benefits. We are also happy to discuss your own needs with you. Feel free to Contact us at info@bioanalyticsgroup.com with technical and purchasing questions, or call 609-632-0091 for additional information.
Key Features, Desktop Version Pathway Drawing Annotation Data and Network Analysis Simulation Import and Export
Additional Features, Server Version Collaborative Annotation Database Support System Level Features
BioPathwise™ 2.0 Features in Detail
Desktop Version: Pathway Drawing Tools for working with Pathways allow your team to: · Manually draw and position new biological entities. · Connect biological entities using reactions/links. · Assign unique shapes to entities (list is extensible). · Zoom in and out to focus on parts of a Pathway, including Zoom to Fit. · Toggle between math names and display names. · Apply auto-layout algorithms. · Add background images to a Pathway. · Change the size of entities, and lock the size. · Wrap the names of entities within the node border. · Turn off node borders. · Create complexes that have other entities as internal parts. · Customize the entity palette for easy entity type selection. · “Find” an entity by its name or partial name and highlight it on Pathway. · Assign names that include spaces, numbers, symbols. · Create shortcuts for entities to aid in layout.
Annotation Communicating your data and its context to colleagues, collaborators, journals, and funders is essential. Embedded in the system are tools for: · Free text annotation. · HTML support in free text pane. · Auto-insert of PubMed and Google searches. · Pasting text-only into annotation pane. · Choosing from numerous pre-defined, structured annotation categories for entities, reactions, and the entire Pathway including species, tissue, biological function, evidence, function, type, state, location. · Viewing Pathway annotations in a table format for easy editing and comparison.
Additional Features Available in the Server License Version: Collaborative Annotation · Customizing annotation categories that are synchronized across an organization. · Easily linking to Molecule Pages and View/Edit Report. · Adding information on molecule pages to store proprietary information along with public data. · Creating links between species on the Molecule Pages.
Data and Network Analysis Extensive capabilities have been integrated to provide: · Network analysis to highlight shortest and complementary paths, and critical points. · Gene expression analysis to infer statistical relationships within a data set. · Fit simulation parameters to attached time series data files. · Tools for attaching time series or categorical data files to a Pathway, then overlaying them directly on the pathway or plotting them.
Simulation Working with complex datasets to develop hypotheses, optimize experimental parameters, and create informative models is the primary utility of BioPathwise 2.0. With features that respond to the needs of the experts who created them, this is a robust solver that adapts well to very stiff problems. With it, your team will be able to easily: · Assign concentrations to biological entities. · Keep entity concentrations fixed (buffered). · Assign kinetics to reactions. · Choose from 17 pre-defined kinetic types (including mass action, Hill kinetics, Michaelis-Menten, Inhibitions, etc), filtered to match the reaction configuration (inputs, outputs, enzymes, etc). · Integrate custom math to describe reaction rates with extensive support tools. · Exclude specific reactions from the simulation. · Source and Sink entities including math support. · Plot individual or sets of entities to display simulation results. · Zoom and edit features on simulation plots. · Visualize simulation results as a color-map directly on a pathway using multiple scaling options. · Adapt experimental protocols that allow simulations to match experimental conditions. · Use graphical tools to design experimental protocols. · Store multiple protocols as separate items for easy sharing. · Apply deterministic and Monte-Carlo protocols. · Control protocols both over time and initial values for entities and rate constants. · Generate automated whisker plots for Monte-Carlo protocols which include distribution statistics. · Construct dose-response curves. · Graphically display system math using mathematical symbols. · Add intermediate variables and new state variables. · Assure unit consistency across datasets.
Import and Export Interacting with publicly available and proprietary data presents special challenges. BioPathwise 2.0 includes tools that allow your team to: · Export the Pathway in multiple image formats. · Export system equations as images or pdf. · Export simulation model as text, as a C model, as FORTRAN, as MATLAB, as CellML. · Export the Pathway and equations along with free text annotation as a set of web pages. · Import CellML. · Import SBML. · Export plots as images.
Database Support Integral to the system are features that allow you to: · Launch View/Edit Molecule information pages from client. · Automatically synchronize client and server annotation meta-data on software start. · Search web pages to identify synonyms and link entities to them. · Save Pathways and all related data files on the server. · Assign read/write permissions to Pathways based on individual/group membership. · Create and organize Pathways by subject. · Browse and retrieve Pathways in the database · Search and retrieve Pathways from the database using many types of annotation to narrow the search · Publish Pathways so that trusted versions can not be modified · Break Pathways into individual reactions and Publish these in the database · Construct de novo Pathways by searching for reactions that connect specified substrates and products. · Automatically paste into a Pathway all interactions in the database involving a specific entity.
System Level Features Working in collaborative research teams requires seamless management of the overall system. BioPathwise 2.0 allows appropriate members of your group to: · Modify site-wide annotation information that is automatically downloaded to all desktop software across the organization. · Create and manage database users, including privileges. · Use a full featured API that allows off-line construction of Pathways, creation of custom importers and auto-layout algorithms, control of simulation variables, running of simulations, capture of simulation results, etc. · Access comprehensive on-line help system that provides detailed instructions on the use of the software. · Take preloaded tutorials to help get acquainted with the software. · Simultaneously manage of the Pathway file and all related data files using projects. · Merge Pathways with software assistance to help identify common entities and reactions and highlight conflicts between Pathways.
For more information, contact The BioAnalytics Group.
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