tellurium | Python Environment for Modeling and Simulating Biological
kandi X-RAY | tellurium Summary
kandi X-RAY | tellurium Summary
Tellurium is a python environment for reproducible dynamical modeling of biological networks. Tellurium provides the interfacial code to convert between standard formats and utilize powerful libraries without requiring technical expertise, allowing you to focus on what’s important: building better models. Tellurium also provides first-class support for exchangeability via COMBINE archives, allowing you to share your models and simulations with other tools. Tellurium combines state-of-the-art scientific Python libraries, such as NumPy and SciPy, and includes special-purpose systems biology Python tools. Out of the box, Tellurium includes libroadrunner, antimony, phrasedml, libsbml, and libsedml. The Tellurium project is funded from the NIH/NIGMS (GM081070).
Support
Quality
Security
License
Reuse
Top functions reviewed by kandi - BETA
- Create plugin actions
- Send a command to the console
- Returns the current editor
- Return the current editor widget
- Register an editorstack
- Clone file and register widget shortcuts
- Initialize a new editor file
- Apply syntax highlighting settings
- Returns the finfo of the current file
- Resolves the model changes in a document
- Simulate the SSE
- Determine if two species have the same species
- Saves the simulation data
- Returns a list of locations for the given format
- Exports this card to a combine
- Calculates distributed sensitivity analysis
- Plot the simulation data
- Parse a dd file
- Convert a data generator to python code
- Generate a graphviz graph
- Execute a combine archive
- Create a window
- Open files
- Plot a scatter plot
- Reads a SEDML document
- Plot an array
tellurium Key Features
tellurium Examples and Code Snippets
Lines of Code : 13License : Permissive (Apache-2.0)
Copyimport tellurium as te
rr = te.loada('''
model example0
S1 -> S2; k1*S1
S1 = 10
S2 = 0
k1 = 0.1
end
''')
result = rr.simulate(0, 40, 500)
te.plotArray(result)
conda install msgpack-python
pip install tellurium
/Users//anaconda3/bin/pip install tellurium
pip install tellurium
pip install git+https://github.com/sys-bio/tellurium.git
Community Discussions
Trending Discussions on tellurium
QUESTION
I wanted to return the name of elements based on two conditions; even protons number and odd neutrons number. I've tried to print both tests and it turns out well. However, when I try to print the elements using 'and' logical, an error has occurred due to different broadcasting. I can't figure out how do I reshape it. Help me out.
The elements, protons and neutrons.
I've already converted elements, protons and neutrons into arrays.
The input;
...ANSWER
Answered 2020-Oct-16 at 15:26Apply the & to the boolean tests, before indexing:
QUESTION
I am trying to streamline the isotope handler in a react component -- I want to create filter options that would be like catergory[metal] or catergory[transition] -- and combo filters like catergory[metal, transition].
the sandbox for this. https://codesandbox.io/s/brave-sea-tnih7
So like filterFns[ filterValue, "param2" ] -- how to push 2 params into the filter functions - rather than these fixed greaterThan50 -- a "greaterThan(50)", "greaterThan(5) -- this dynamic filtering type of handler "
latest sandbox https://codesandbox.io/s/brave-sea-tnih7?file=/src/IstotopeWrapper.js
...ANSWER
Answered 2020-Oct-11 at 04:07In you application you can stor filters inside an array and update filters array to either new filter (single filter mode) or push newly selected filter on top of existing filters list.
Take a look at updated codesandbox here.
First of all we are registering our filter method with Isotope:
QUESTION
I am really new to Scala. I tried to mock a simple Scala function using Mockito, but I get the following error. I have checked the internet but I was unable to find out the error.
...ANSWER
Answered 2017-Sep-13 at 04:55You cannot mock objects, try to move your code to a class:
QUESTION
So I've been working on this program for a while and I have gotten it to a point where it compiles just fine but when I run it I get a Segmentation Fault. I've backtraced the fault via gdb to the function below but cannot for the life of me see where the problem is, and I am not versed enough with gdb to determine any more details on the origin of the fault. Like the question says I'm trying to read from a file into a dynamically allocated linked list where each node of the list has a pointer to a struct called Element. Then I need to convert that linked list to an array of pointers to struct Element. I hope that a fresh pair of eyes can see some mistake I've made that I have been blind to.
UPDATE: Added rest of source files. Added gdb backtrace snippet.
Element.h
...ANSWER
Answered 2018-May-09 at 06:25The good news is you were really, really close. The bad news is the "really really close" part -- it only takes one subtle error to torpedo your code.
First the general discussion. While there is nothing wrong with using a pointer-to-pointer-to-Element, you are missing the benefits of using C++ and the automatic memory handling offered by . That said, it is good to know how to handle both.
Your error is:
QUESTION
I've just upgrade my project to Angular 4.0.0 and Angular CLI 1.0.0 from Angular 2.4.7 and Angular CLI 1.0.0-beta.31. Since upgrading I am getting the following errors:
...ANSWER
Answered 2017-Mar-25 at 07:19Have a look at this official release notes the folder structure is changed and you should be changing the path as
QUESTION
I am new to Spark and I am trying to create an RDD from the Hadoop sequence file. But I am getting the following error. I have searched it from the online articles but failed to sort it out with the given solutions. So can anybody please help me to resolve this?
My pom file is like this,
...ANSWER
Answered 2017-Jan-18 at 05:32I was able to resolve this issue. Actually it was caused by the incompatible versions of the jackson library. I am using spark 1.6 version along with Hadoop 2.6. I have used the jackson-databind version 2.4.4. That was perfectly resolved my issue. Below dependency resolved that incompatibility. Previously I have used 2.2.4 version which made the issue.
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install tellurium
Binary pip packages for Tellurium are available from PyPI and support 64-bit Python versions 3.6, 3.7, and 3.8 for Windows, Mac, and Linux. Pip packages are tested on Fedora 22, Debian 8, Ubuntu 14.04, and Mac OS X 10.13. The latest package release can be installed via. For developers, the latest stable version from the repository can be installed via.
:exclamation:If you would like a detailed instruction on how to setup Tellurium on Anaconda distributions, check this page.
Download the Anaconda distribution for your platform.
Follow the installer instructions.
When prompted, add Anaconda to your PATH
Run
Support
Reuse Trending Solutions
Find, review, and download reusable Libraries, Code Snippets, Cloud APIs from over 650 million Knowledge Items
Find more librariesStay Updated
Subscribe to our newsletter for trending solutions and developer bootcamps
Share this Page
