Frequently Asked Questions
For Labs & Vendor Partners
MarkerLab is web-based software that simplifies the management, organization and visualization of omics data. MarkerLab users can access or create a virtually limitless collection of data organizing tools including ontologies, pathway maps, annotations, and algorithms. These resources are quickly and easily combined with unique user insights to create a dynamic knowledge base for individuals and institutions.
When your MarkerLab services are deployed, you have immediate access to core functionality across the platform. You can load your clients’ final data and supporting documentation, distribute study invitations to client users, and maintain active communication via dashboard messaging and collaborative note-taking functionality.
In addition, MarkerLab offers extensive customization so you can tailor your solutions for each individual client. Create or modify pathway maps to support the data offering, author and edit the underlying ontologies used in enrichment and signal detection algorithms, and associate sets with public resources—or create them individually according to your preference.
Yes, sign up for a free MarkerLab account and we’ll email your invitation to a public demo study. Use the invitation link to log in to your account and access the demo study. Please reach out with any questions or comments along the way, we appreciate your input.
When you’re ready to take the next step and load your own data into MarkerLab, you can request a service agreement, or contact us via email. We’ll be happy to answer questions or talk with you about MarkerLab account options.
MarkerLab is a web application that runs in most modern web browsers on both Apple and PC-based operating systems.
Yes, MarkerLab includes annotations for individual biomarkers mapped to database IDs from Uniprot, Ensemble, Pubchem, HMDB, and KEGG. MarkerLab also includes sets and pathways derived from Reactome.org, with integrated functionality that allows you to create, edit, and share your data organization strategies across the platform.
MarkerLab provides beautiful, dynamic reporting with multiple levels of data interaction and evaluation. You can review experimental effects across the entire data set, at the pathway and marker set level, or in detailed data cards that describe specific effects on individual markers.
In the current release, MarkerLab data visualizations include:
- Bar Plot
Sort markers by difference between selected groups, choose individual markers to view additional detail and data, and identify pathways and sets of interest using enrichment and signal detection algorithms.
- Volcano Plot
Plot markers by significance and degree of difference, and filter them by sets. Export reports of marker candidates based on user selections and use the results to create new sets that can be stored and reused in future studies.
- Pathway Maps
Visualize study data in a curated collection of multi-omic enabled pathway heat maps.
Additional reports are currently in development, including PCA/PLS-DA, ROC, and Clustering Heat Map. Users receive immediate access to new reports as they are launched.
Yes, currently you can download the marker and meta data used in each study as well as any files attached to the study. Additionally, you can download spreadsheets of markers meeting certain statistical qualifications from reports, for instance the “cut-list” from volcano plots. MarkerLab will include additional functionality to export marker card and report images in future release.
The MarkerLab platform includes exceptional flexibility to meet your specific requirements, and we offer proven technology and research expertise to help you design and build custom solutions tailored to your objectives.
Our consulting services include:
- Integration of your preferred ontologies, annotations, reference databases or sources of pathway maps
- Tool modifications to support alternative statistical approaches, and custom algorithms designed to run on your data
- Design and development of additional data visualization and reporting tools to support your offering
- Implementation of custom marker annotations, linked to external web pages or catalog IDs
Yes, the MarkerLab reporting environment supports brand integration for labs and partners—including prominent placement of your corporate identity, and accompanying visual design modifications to further differentiate your studies and represent your brand. In effect, the MarkerLab visual design framework allows you to use the platform as your own ready-made client tools offering.
About Your Data
MarkerLab works with your final study data (marker names and concentrations), and is designed to help researchers move from a completed data set into discovery and understanding, quickly. The MarkerLab platform supports multi-omic data integration and is particularly useful for metabolomics, lipidomics, proteomics, and transcriptomics data. There is currently no functionality for displaying or organizing sequence data.
After upload, your experimental data are matched to public database IDs and presented in MarkerLab studies. Within each study, MarkerLab provides simple controls that allow you to define experimental groups for comparison, add and edit collaborators and permissions, and view interactive reports. As long as your account remains active, all of your study data (including meta data and any documentation that you provide to aid in the interpretation of the experimental design) remains conveniently accessible and available for download.
Yes, MarkerLab supports additional data uploads and data file replacements. In the event that you need to upload additional study data, your new file will be merged with the existing data set (provided that both sets of data share matching sample IDs). If you prefer to replace all of your study data, you can simply upload a new comprehensive data file.
You own your data so it is always in your control. From your study settings, you can modify or revoke collaborator access to your data at any time, and MarkerLab will never sell or provide access to your data to any other party without your consent.
You own your data and only you can determine who will access your MarkerLab studies. MarkerLab may perform analysis on anonymized and aggregated data across the platform, but only for the purpose of enhancing our products and services. We will never sell, share, or use your study data in any commercial context outside of the platform.
Our cloud-based platform utilizes industry-standard practices to ensure that your MarkerLab data is accessible only to you and those you authorize, is kept highly available and is reliably backed up.
Our layered security approach includes data center physical security, operating system level security, firewalls, user authentication and authorization, and controlled access to the production data environment. Regularly scheduled data backups ensure that your data is always protected. And our scalable infrastructure means your data is always available to you.
Personal identities are only revealed when users engage in “opt-in” activities. Examples include: posting notes which can be seen by collaborators on a study, or sending email (initiated on the MarkerLab Platform) for the purpose of inviting collaborators to participate in research activities.