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Description

Cufflinks is a software tool that compiles transcripts, estimates their levels of abundance, and evaluates differential expression and regulation in RNA-Seq datasets. By accepting aligned RNA-Seq reads, it organizes these alignments into a streamlined representation of transcripts. The software then assesses the relative abundances of these transcripts based on the number of supporting reads, while also factoring in potential biases from library preparation methods. Initially created through a collaboration with the Laboratory for Mathematical and Computational Biology, Cufflinks aims to simplify the installation process by offering several binary packages that alleviate the often cumbersome task of building the software from source, which necessitates the installation of various libraries. This toolset encompasses multiple utilities tailored for analyzing RNA-Seq experiments, with some functionalities available independently and others designed to fit into a more comprehensive workflow. Overall, Cufflinks serves as a vital resource for researchers in the field of genomics, enhancing their ability to interpret RNA-Seq data effectively.

Description

Tellurium is a versatile Python package that integrates several key tools necessary for conducting simulation studies in systems biology and various other fields. It offers access to the robust high-performance simulation engine known as libRoadrunner. Users can create their models using Antimony, a simplified, human-readable format based on SBML. Additionally, an Antimony tutorial is available for those looking to learn the specifics of the language. Tellurium is compatible with all major standards, including SBML, SED-ML, and COMBINE archives. It can be utilized through user-friendly GUI environments like Spyder, PyCharm, or Jupyter Notebooks, including CoLab, which enhances productivity and supports interactive editing features. Installation is straightforward, achieved through the standard pip method, and there is also a convenient one-click installer available for Windows users that sets up a comprehensive environment for systems biology modeling. The development of Tellurium benefits from the contributions of a wide range of open-source developers, ensuring a continually evolving tool for researchers. Overall, Tellurium stands out as an essential resource for those involved in simulation studies across multiple scientific disciplines.

API Access

Has API No 

API Access

Has API No 

Screenshots View All

Screenshots View All

Integrations

No details available.

Integrations

No details available.

Pricing Details

Free
Free Trial No 
Free Version Yes 

Pricing Details

$15.00/month/user
Free Trial Yes 
Free Version Yes 

Deployment

Web-Based No 
On-Premises No 
iPhone App No 
iPad App No 
Android App No 
Windows Yes 
Mac Yes 
Linux Yes 
Chromebook No 

Deployment

Web-Based Yes 
On-Premises No 
iPhone App No 
iPad App No 
Android App No 
Windows No 
Mac No 
Linux No 
Chromebook No 

Customer Support

Business Hours No 
Live Rep (24/7) No 
Online Support Yes 

Customer Support

Business Hours No 
Live Rep (24/7) Yes 
Online Support No 

Types of Training

Training Docs Yes 
Webinars No 
Live Training (Online) No 
In Person No 

Types of Training

Training Docs No 
Webinars Yes 
Live Training (Online) Yes 
In Person No 

Vendor Details

Company Name

Cole Trapnell

Founded

2017

Country

United States

Website

cole-trapnell-lab.github.io/cufflinks/

Vendor Details

Company Name

Tellurium

Founded

2010

Country

United States

Website

tellurium.analogmachine.org

Product Features

Automated Testing

Hierarchical View No 
Move & Copy Yes 
Parameterized Testing Yes 
Requirements-Based Testing Yes 
Security Testing No 
Supports Parallel Execution Yes 
Test Script Reviews Yes 
Unicode Compliance No 

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