Welcome to PULSE, our monthly round-up of what's new in Mass Dynamics - one connected platform, doing more with your data every month.

The theme this month: reading your biology, more ways.

• A new way to run your pathway analysis: more knowledge databases and more analysis settings
• New views that connect your results: link not only single entities but also different omics layers
• More control over how you present them: personalize colors and rendering

Here's what's new.

0 1 · N O W  L I V E

Over-Representation Analysis

You already had GSEA for pathway enrichment. Now you can also create Over-Representation Analysis (ORA) datasets. ORA asks which pathways are over-represented in your list of changing entities. This unlocks a fast, intuitive view of the biology behind your data and stores the results so you can reuse them across tables and visualizations. This is how it works:

• Run ORA as a dataset. Point it at a list of interest and get enriched pathways back. You now have access to an expanded list of biological databases, and you can tweak the reference universe your list is tested against.
• A new ORA dot plot. View which pathways are enriched, how significant they are, and how many entities drive each result.
• Sits beside GSEA. Two ways to read the same biology, side by side.

0 2 · N O W  L I V E
More ways to visualize and connect your results

A set of new modules to move from "these things changed" to "here's how they relate": this is the connected view your data has been building toward.

• Entity Map. See how entities across your data - such as proteins, peptides, genes, and PTMs - are connected. Explore these relationships as an interactive graph or directly while visualizing and analyzing your data. For example, identify proteins changing in one analysis and connect them to the corresponding genes identified in another.
• Cytoscape integration of the PPI network graph. Protein-protein interaction networks with richer per-node and per-edge interactivity and statistical overlay.
• Multi-Omics Factor Analysis (MOFA) variance-explained heatmap. See which factors drive variance across all your omics layers.
• PTM Identifications Bar Plot. Visualize your dataset modification landscape at a glance across chosen conditions.

Less staring at a table, more following the biology.

0 3 · B E T A   R E L E A S E

More control over how your plots look

Custom color palettes. Set personalized colors for the conditions labeled on your heatmaps and dimensionality reduction plots.

This feature is a beta release. Want it switched on for your workspace?

👉  Just reply and we'll switch it on - we read every one.

0 4 · A G E N T - R E A D Y 

New skills for your agent

For those driving Mass Dynamics with an AI agent: we've added transcriptomics skills, so your agent can run gene-expression workflows the same reproducible way you would in the app. Access all the new skills:

1. Download the Agent Pack
2. Set it up with your agent of choice
3. Start analyzing

0 5 · T H R O W B A C K   F E A T U R E 

Predictable pricing by design. Ask more, pay the same.

One thing ties all of this together: it's all included.

Mass Dynamics is a single annual subscription with upfront pricing, so whether you're running ORA today, WGCNA and transcriptomics tomorrow, or using AI agents across your workflows, your Mass Dynamics costs stay predictable.

Science rarely ends with the first question. When every analysis comes with an extra cost, researchers naturally ask fewer questions. We think discovery works better when you don't have to think twice about running the next analysis.