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Cellucidate Support Feb 09 • New! RuleStudio for Cellucidate
We are proud to announce the alpha launch of RuleStudio for Cellucidate!
RuleStudio is a desktop application designed specifically for writing and editing for Kappa files. It includes features that make writing Kappa quicker and easier, while still providing the specific benefits of Cellucidate.com.
Product Highlights
- Streamlined Model Coding. Write Kappa in an environment that explicitly understands the nuances of the language, and even includes auto-complete functionality, making the process of creating a model much faster.
- Problem Identification. Gain insight into what problems may exist in your model, even before simulating it: automatic error checking, visualization tools that show you what you’ve built, and simulations to validate results.
- Model Organization & Navigation. Avoid the need to arrange your files in an organized manner. Files are automatically organized by RuleStudio, with built in features that allow you to easily navigate to specific areas of your models.
- View Customizer. Change the location and size of the windows in your application, so it’s easier to see what is most important to you.
- Seamless Cellucidate Integration. Get access to advanced capabilities only available on Cellucidate.com (multiple simulation runs, graphical editor, publish model), with the quick click of the “Upload to Cellucidate” button.
This video gives you a short intro to RuleStudio:
We invite you to take RuleStudio for a spin and send us your feedback! If you have already received an invitation, you can download the application from your profile page (look for the "Cellucidate Rule Studio" tab). You can send us feedback by submitting a request here in our support center, or by emailing us at support@cellucidate.com.
If you do not already have access to RuleStudio, but would like to try it, please email us at support@cellucidate.com.
Cellucidate Support Nov 24, 2009 • Getting Around Cellucidate
Hello,
Welcome to the Help and Support page for Cellucidate. Use this space to learn about Cellucidate and creating content using Cellucidate tools, request help on troubling issues, suggest new features, and begin discussions with the Cellucidate community about topics ranging from modeling to biology.
Diving Into Cellucidate - Using Help Resources:
You can always access these topics easily by using the links in the right side panel.
- New to Cellucidate? Read topics in Getting Around Cellucidate to orient you to the Cellucidate website and how to maneuver around it. Information on how to navigate around your own personal account can also be found there.
- Exploring Cellucidate. Wondering what a specific icon or a feature on Cellucidate means? Read the Reference Guide to better understand the many features and capabilities available on Cellucidate.
- Making Successful Models. If you are ready to start creating content and models in Cellucidate, read material in Building Models in Cellucidate to understand model creation process and the way to create a successful, running model of your biological system.
Have a Specific Question? A Troubling Issue?
Check out our dynamic FAQ section to see if your question has been addressed. If it hasn't then you can pose the question to the entire Cellucidate community on the Discussion Forums or personally contact the Cellucidate Team by filing a request.
If you want to suggest a new feature to us or are encountering problems on Cellucidate, we would love to hear from you! Create a new request using this website. We encourage users not to hesitate in personally connecting with the Cellucidate Team via the request system.
Cellucidate Support Nov 24, 2009 • Getting Around Cellucidate
Cellucidate is a collaborative, web-based modeling platform designed specifically around the needs of biomedical researchers working in cell signaling and cellular information processing or other quantitative approaches. Driven by the recognition that there is a great unmet need for modeling methodologies that are applicable to complex biological systems, Cellucidate offers researchers (even those with little or no prior exposure to biological modeling) the functionality to build an intuitive, transparent and flexible way to integrate expermintal data into dynamic models in which the causal and temporal properties of complex cellular systems can be explored. Cellucidate's intuitive models can leverage the value of the wealth of existing data by providing mechanistic insights into experimental observations. Cellucidate can be an invaluable and complementary approach to lab work for experimental biologists, offering researchers an intellectual framework in which to make sense of their laboratory data and enabling them to generate and test hypotheses and to design more focused experiments.
Cellucidate's web-based design provides a connected, collaborative workspace in which data and models can be shared within an online scientific community, and its use of server cloud technology effectively brings the necessary computational infrastructure directly into the researchers' laboratories, allowing them to focus their valuable resources on their laboratory work. Given the complexity of cell biology and the vast amounts of experimental data being generated, collaboration will be a key ingredient for future progress in the field and Cellucidate facilitates research collaboration on a national and even a global scale.
Cellucidate can help you:
- Define, Explore, and Execute your Model - Select or create the "players" in your model (agents) and their interactions and state changes (rules). Then navigate your model's interactome (contact map) and trace its causal structure (influence map). You can then explore the casual relationships between different species (stories) and run simulations to dynamically trace abundances of specific species.
- Collaborate on your Model with Others - Work with one or many people to simultaneously edit, build and or
execute your model. You control who has editing privileges and for how long they can edit. We provide you with a book history to better track changes to your model, and you can also use Cellucidate to send/receive important and private messages between you and your collaborators.
- Organize Your Model - The cBook is self contained and is designed to organize large modular systems. It's easy to move pieces around, rename and navigate through large parts of your model. Bookshelves allow you to easily manage multiple projects at once. Additionally, models can be supported with annotations and journal pages to better communicate your approach within the model and to link directly to the literature.
- Distribute your Model to the Community - Make your model public to the world or just the Cellucidate community and allow users to comment and explore your created content.
This video presents a brief demonstration of the use of the Celucidate web-based workspace for biological modeling. It should be noted that some of the UI features for the beta version of Cellucidate shown in the video have since been updated and look different in the current version of the platform.