Announcing Dash Bio 1.0.0
To install Dash Bio, run the following commands below in your Terminal/Command Line:
pip install dash-bio
Dash Bio is a one-stop shop for bioinformatics and drug development visualizations. It contains a suite of components and tools to parse and visualize files from common bioinformatic databases. Since its release, Dash Bio has grown in popularity within the scientific community, with over 400 stars on Github. Dash Bio 1.0.0 results from listening to your requests for simplification and optimization. It offers new ways to parse data files, has increased the performance and feature list of old components, and includes the release of new components.
Major Dash Bio Upgrades:
- Dash Bio Utils is integrated with Dash Bio
- All Molecular components support PDB, mmcIF
- New component: JSME
With 1.0.0, we resolve some of the friction users experienced with Dash Bio by integrating Dash Bio Utils and changing parameters and configurations to be friendlier and more semantic. Essentially we’re taking all that we’ve learned from our community and making Dash more intuitive and robust for years to come. In Dash Bio 1.0, Dash Bio Utils is fully integrated, meaning that using Dash Bio only requires downloading the Dash Bio package. Dash Bio Utils contains a set of helper scripts that work together with the Dash Bio and previously needed to be downloaded every time to work with Dash Bio.
To install Dash Bio, run the following commands below in your Terminal/Command Line:
pip install dash-bio
Parsing More Files!
One of the most significant additions to Dash Bio 1.0.0 is the support of more filetypes and examples. To maximize scientific discovery and usability, we drove changes so that components within the same subclass e.g. molecular rendering, sequence viewing, could take in the same input type. As we expanded what each component could parse, we also added an example data section within its’ Dash page that links data from scientific sources for users to try out and explore themselves.
All components in molecular data now support PDB and mmCIF files. Adding these file types to Dash Bio gives more flexibility to interpret a molecule’s thermodynamics, kinetics, and geometric properties. Each file contains atomic coordinates, secondary structure, and atomic connectivity, which Dash Bio can use to model protein structures for use cases such as drug discovery or to create more efficient biocatalysts for industrial applications. PDB and mmCIF files can be obtained from the Protein Data Bank — a global repository for exploring and downloading molecular structural data.
Alignment Chart and Sequencer Viewer both take in FASTA files. These subplots can help with quality control. With Quality Control reports, you can detect problems with laboratory processes (uneven pooling, high ribosomal RNA content), improve protocols, compare results to previous experiments and reduce cost.
New Component: JSME
To increase understanding of chemoinformatics, we have added a JSME component to enable users to draw molecules and chemical reactions. Knowing a molecular structure informs us of the polarity, reactivity, phase of matter, color, magnetism, and biological activity. The chemical structure representations can be manipulated in 2D space. The component wraps the BSD licensed JSME molecule editor (by B. Bienfait and P. Ertl) in a React component for easy use in React apps. The editor is able to export molecules as SMILES, MDL/Symyx/Accelrys Molfile or in its own compact format. Full documentation on how to draw, edit, query atoms, and keyboard shortcuts can be found on the JSME homepage. The addition of JSME expands the types of molecular rendering Dash Bio offers and showcases reaction inputs which were previously not available with current components.
Enhancements
Dash Bio components have been upgraded for performance and feature enhancement. AlignmentChart and Circos have had the most significant performance lift for faster rendering and to ensure that all features work as expected. New feature requests have been focused on molecular rendering components. Molecule3DViewer has new zoom features. The feature zooms in with a constant factor and maintains the rotation and orientation of the stage while zooming while keeping any selections or property changes from other callbacks. Speck now offers you to customize your labels to the viewer. NGLMoleculeViewer can visualize multiple molecules and now has an additional feature that allows molecules to be represented either side-by-side or intertwined.
What’s Next?
Dash Bio components build on each other, and you can quickly and easily create your own dashboard for deeper insights. As we continue to grow, we would love your insight into what components you like the best and features you want to see.
💊 If you’re a researcher, lab, chemical company, or drug development company, and you would like a customized Dash app or component built for you, please get in touch — we love a challenge.
If you like where we’re going with Dash, head over to our freshly minted GitHub project and give it a star! 🌟 https://github.com/plotly/dash-bio. And Check out some more Dash Bio apps in the Dash Gallery!
We also love giving Dash trainings if you’re re-thinking how analytics is done at your organization. Dash is an easy first Python library to learn, and we can help your team boost productivity.
For more information, email us at info@plotly.com!
