JupyterLab
Project Jupyter exists to develop open-source software, open-standards, and services for interactive computing across dozens of programming languages. JupyterLab is a web-based interactive development environment for Jupyter notebooks, code, and data. JupyterLab is flexible, configure and arrange the user interface to support a wide range of workflows in data science, scientific computing, and machine learning. JupyterLab is extensible and modular, write plugins that add new components and integrate with existing ones. The Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations and narrative text. Uses include, data cleaning and transformation, numerical simulation, statistical modeling, data visualization, machine learning, and much more. Jupyter supports over 40 programming languages, including Python, R, Julia, and Scala.
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Tellurium
Tellurium is a Python package that knits together a variety of important packages for carrying out simulation studies in systems biology and other disciplines. Tellurium provides an interface to the powerful high-performance lib roadrunner simulation engine. Tellurium allows you to build your models using an easy-to-use human-readable version of SBML called Antimony. Antimony Tutorial. Tellurium supports all the major standards such as SBML, SED-ML, and COMBINE archives. Tellurium can be used via GUI front-ends such as Spyder, PyCharm, or Jupyter Notebooks (including CoLab) with support for advanced productivity and interactive editing features. Installation is via standard pip installation. We also provide a one-click installer for Windows users which provides a complete environment for systems biology modeling. Tellurium relies on open-source contributions from many people.
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Artelys Knitro
Artelys Knitro is a leading solver for large-scale nonlinear optimization problems, offering a suite of advanced algorithms and features to address complex challenges across various industries. It provides four state-of-the-art algorithms: two interior-point/barrier methods and two active-set/sequential quadratic programming methods, enabling efficient and robust solutions for a wide range of optimization problems. Additionally, Knitro includes three algorithms specifically designed for mixed-integer nonlinear programming, incorporating heuristics, cutting planes, and branching rules to effectively handle discrete variables. Key features of Knitro encompass parallel multi-start capabilities for global optimization, automatic and parallel tuning of option settings, and smart initialization strategies for rapid infeasibility detection. The solver supports various interfaces, including object-oriented APIs for C++, C#, Java, and Python.
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Bokeh
Bokeh makes it simple to create common plots, but also can handle custom or specialized use-cases. Plots, dashboards, and apps can be published in web pages or Jupyter notebooks. Python has an incredible ecosystem of powerful analytics tools: NumPy, Scipy, Pandas, Dask, Scikit-Learn, OpenCV, and more. With a wide array of widgets, plot tools, and UI events that can trigger real Python callbacks, the Bokeh server is the bridge that lets you connect these tools to rich, interactive visualizations in the browser. Microscopium is a project maintained by researchers at Monash University. It allows researchers to discover new gene or drug functions by exploring large image datasets with Bokeh’s interactive tools. Panel is a tool for polished data presentation that utilizes the Bokeh server. It is created and supported by Anaconda. Panel makes it simple to create custom interactive web apps and dashboards by connecting user-defined widgets to plots, images, tables, or text.
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