We are entering an exciting era of multi-omics! Every day we wake up with very new and different omics data generated along with bioinformatics methods, algorithms, and AI developed at an extremely fast pace. Looks good already, doesn’t it?
Not quite. Drug development organizations are facing the challenges of keeping up with state-of-the-art methods for their current workflows and infrastructure in order to leverage multi-omics data. With platforms that cannot adapt, this is hard to achieve.
With that in mind, Pythia Biosciences developed CDIAM, a microservice-based multi-omics analysis software platform on the web with speed of development, adaptability, and customization. CDIAM owns a microservice-based architecture and a command-line interface that enable bioinformaticians' speedy customizations, along with a graphical user interface accessible to all biologists.
In this article we will introduce you to the CDIAM multi-omics analysis software platform, what it is, and why you need to choose it for your multi-omics projects.
What is CDIAM?
CDIAM, or CDIAM Multi-Omics Studio, is a microservice-based SAAS platform for multi-omics analysis with speed of development, adaptability and customization.
CDIAM stands for “Carpe DIAM” meaning to seize the Data, Interactome, Algorithms and Machine Learning. The platform takes in data and analysis results from various types of omics such as Genomics, Transcriptomics, Proteomics, Epigenetics, Metabolomics, Microbiome, Interactome, Single Cell, and Spatial data. Inputs can be as simple as a gene/protein table, a DE result, or an expression matrix.
Why choose CDIAM as your multi-omics analysis software?
1. Simple deployment and access
CDIAM is an SAAS framework - meaning no installation. You can access the platform anywhere via common web browsers: Chrome, Firefox, Edge, Safari, you name it. The platform can be deployed either behind your organizations' firewall or using private cloud configurations.
2. Microservices for customization and graphical user interface for ease of use
The microservice-based architecture of CDIAM enables bespoke development, integration with public or internally built pipelines and tools (like R shiny data visualization applications) or even the ability to bring CDIAM capabilities to existing in-house computational resources.
To unite bioinformaticians and biologists, CDIAM also presents itself in an intuitive GUI.
3. Multi-omics data management and aggregate analysis, all in one place
The platform manages the data as individual datasets or groups them in ‘projects’. Multi-omics data in a ‘project’ can be collectively analyzed for aggregate insights, or individually explored. Examples of such aggregate insights include: top ligand-receptor pairs, top cell types interacting with each other, overlapping significant pathways, potential targets, etc. commonly found across experiments.
4. Customizable workflows for biomarker validation and target discovery
Among the key highlights of CDIAM are the Pathway2Target and Biomarker2Validate workflows. As you can tell from the name, the workflows support you to identify, systematically score, and rank targets or biomarkers with the input being a list of significantly enriched pathways. You can choose from common workflow templates or customize your own.
In addition to targets and biomarkers, we are also developing Safety, PD Biomarker, Mechanism of action, and experiment planning workflows.
5. Enriched pathway analysis
CDIAM supports you with an interactive GUI to easily run and explore enrichment. Feel free to choose from the default gene sets like Reactome and NCIv2 PID or import your custom gene sets.
6. Intercellular signaling prediction, pipelines, and more
For single-cell data, CDIAM supports cell-cell signaling with default CellphoneDB integration. You can run one or multiple intercellular signaling predictions on different samples and compare results among them quite easily. Wondering whether it can integrate another cell-cell interaction method on your wish list? It sure can!
Aside from that, CDIAM aids your study with the ability to build your own pipelines and validate insights across external public databases.
Let’s “Carpe DIAM”
CDIAM is currently available for trial. Feel free to contact email@example.com to request access to the platform or go to the link below.