Tuesday, July 7, 2015


With Visinets Inc. we have developed a novel tool for graphical modeling of signaling pathways, Visinets.  This tool allows for both modeling and visualization of biological networks in a user-friendly format. The Visinets mathematical approach is based on causal mapping (CMAP) with simplified ODEs that have been fully integrated with graphical interface.  It offers more competent analysis of pathway dynamics than VisiPaths.

For more details refer to our recent publication: Spychala J, Spychala P, Gomez S, Weinreb GE. Visinets: A Web-Based Pathway Modeling and Dynamic Visualization Tool. Yoon B-J, ed. PLoS ONE. 2015;10(5):e0123773. doi:10.1371/journal.pone.0123773.


Sunday, February 26, 2012

VisiPaths - Updated Signaling Pathways Visualizer and Simulator

We'd like to announce an update to our rule-based pathways visualization tool which allows you to follow signaling pathways as they propagate through the cellular networks. 
Unlike other tools, we've built VisiPaths to be fully interactive so that the user can alter any node property and visualize the changes it causes to signaling outcomes. The user can also set any node action in a time-like fashion, using complex constructs such as adding a delay function for a specific connection. 
And we've worked hard to build a complex and powerful toolset that allows you to separately configure and set early signaling events (such as protein phosphorylation/acetylation, etc) and late (transcription) signaling events . And once you configure a pathway, the VisiPaths app will do the hard work of automatically visualizing its oscillations.
To sum up, the main benefits of VisiPaths are three fold:
  1. VisiPaths can map a complex array of connections (interactions) that account for a great number of interacting scenarios
  2. VisiPaths supports nodes with unknown kinetic characteristics (inferred indirectly from cell and animal studies).
  3. VisiPaths provides a powerful interactive graphical platform to assemble pathway maps in an intuitive way. And to help users get started, VisiPaths includes several pre-assembled pathways which could be further altered by the user.
We invite you to check out the app at VisiPaths.com

Wednesday, February 9, 2011

VisiPaths - Signaling Pathways Visualizer and Simulator

As a special Valentines day present to all our users we'd like to introduce the beta of VisiPaths.com!

VisiPaths allows users to visualize cellular signaling pathways as they propagate through the network. The app allows the user to track
  • signal transduction
  • signal crosstalk
  • pathways interactions
  • other systems biology modeling
  • and more!
Once a pathway is loaded and setup, the user can also alter any node properties, including activity and connections, and visualize the changes it causes to the signaling pathways - all in realtime.

With the ease of using a standards compliant web-app, you can modify any parts of the pathway including adding new nodes and creating new connections/interactions to test how they would affect overall signaling pathways.

All node actions can be based on a timer using delay function for each connection. This allows to see separately early (protein phosphorylation) and late (transcription) signaling events and also allows to visualize oscillations.

The app is available as a limited beta to the general public. We invite you to visit VisiPaths.com and signup for an account now.

Monday, January 3, 2011

ScienceSlides Online Improvements

With the new year we are extremely happy to announce a few ScienceSlides Online improvements that we just launched this afternoon.

  • Faster and better search. With the new change you will be able to search though titles and tags of the slides, but also the reference synopsis. We hope that with this addition you'll find it easier to find the slides that you are looking for.
  • Performance improvements. Faster load times - no more waiting!
  • FREE Wednesday Slide download is back online with a little twist. Now we'll ask you to "pay with a tweet" before downloading to spread the word about ScienceSlides content.
  • Various backbend changes to support our new VisiPaths product which we are releasing very soon. We're very excited about 2011 and can't wait to show you what we have been working on.
Stay tuned.

Monday, May 31, 2010

ScienceSlides 2010 - 13th Edition

We are happy to extend out commitment to the scientific community by announcing our updated suite of products with ScienceSlides 2010.

For this latest release, our content has been further expanded and updated. Many fields have been revised, including mTOR protein, Ion Channel physiology, Calcium Homeostasis, Cytoskeleton, mRNA processing, Growth Factor, Tumor Suppressor and Oncogene signaling, TLR and Fcgamma signaling. Significant expansion has been made in Molecular Pharmacology and Medicinal Chemistry.

As always all slides are available in PowerPoint (PPT) format which is compatible across all major operating systems and presentation tools.

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