Projects and Software from HeartBD2K

A collection of powerful tools developed by the investigator teams of our BD2K Center.

01. O-PTM Biology Project

Oxidative post-translational modifications (O-PTMs) of proteins are highly prevalent cellular features that enable diverse and nuanced functions, and elicit critical effects on human health and disease. Thus far, at least 35 different types of O-PTMs have been reported in various model systems and in humans (link). Our project aims to comprehensively characterize the molecular landscape, elucidate mechanistic insights, and define the translational value of O-PTMs in biomedical processes, cells, organelles, model systems, and humans.

02. COPaKB

COPaKB was first conceived in 2008 and released to the scientific community in 2009, demonstrating the longstanding commitment of the UCLA investigator team to Data Science. COPaKB is a cardiac specific knowledgebase that provides a unique resource for remote-access protein identification and relational data analysis between omics datasets and existing phenotype and biomedical knowledge.

03. PathwayPortals

The Reactome PathwayPortals platform is a suite of network analysis tools for performing and visualizing topology analysis and over-representation analysis of gene and protein networks.

04. Sage Synapse

Sage Synapse is a cloud-based collaborative data workspace that allows users to aggregate, describe, and share research progress and data analysis.

05. MetaboLights

MetaboLights is a public database dedicated for the submission and sharing of metabolomics experiments, derived spectra, biological roles and derived information. It also provides search services based on spectral similarities and chemical structures.

06. Integrated Proteomics Pipeline (IP2)

IP2 is a cloud-based proteomics data analysis platform that allows users to upload raw data remotely and perform fast protein identification (ProLuCID) and quantitation (Census).

07. Omics Discovery Index

The Omics Discovery Index (OmicsDI) provides dataset discovery across a heterogeneous, distributed group of genomics, proteomics and metabolomics data resources spanning eight repositories in two continents and six organisations, including both open and controlled access data resources.

08. ProteoSeq

ProteoSeq is a proteogenomic software and statistical framework to process deep RNA-Seq data and generate customized protein databases for experimental identification of protein-level evidence of alternative splicing, RNA editing, or other coding variants.

09. Aztec

BD2K Aztec is a global biomedical resource discovery knowledgebase that allows users to simultaneously search a diverse array of tools. The resources indexed include web services, standalone software, publications, and large libraries composed of many interrelated functions.

10. BioTurn / ProTurn

BioTurn / ProTurn is a software application for analyzing protein turnover dynamics, with web APIs that connect to existing datasets and knowledgebases including COPaKB.

11. BD2KPubMed

BD2KPubMed is a software tool that employs publicly available data to analyze scientific trends and research directions in a particular field of interest.

12. BioGPS / GeneWiki

BioGPS serves as an interface for crowdsourced omics research by providing a user-customizable portal with aggregate information on gene annotations, gene list analysis, and tailored reports. GeneWiki is an ambitious project that translates human gene information into systematic Wikipedia articles. It is fast becoming one of the first sources of information for scientists seeking gene annotations.

Tools in Development

01. ExpressionInterface

A unified query system for integrated data discovery and retrieval across multiple repositories of gene, protein and metabolite datasets including ProteomeXchange, MetaboLights, and the European Genome-phenome Archive.

02. Embassy Cloud

A dedicated cloud infrastructure that couples data access to powerful computational analysis of omics datasets.

03. Text-Miner

A text-mining algorithm to retrieve biologically relevant knowledge from the biomedical literature and format them into structured and computable infoboxes.

04. Big Data Games

Big Data Games (BDG) is a series of interactive games for public outreach and education on the basics of data sciences in biomedical research.

05. MetProt

MetProt is a cloud-based platform for quantifying, triaging and analyzing large-scale, multi-dimensional omics datasets, finding existing as well as novel connections between proteins and metabolites, annotating molecular functions, and providing biomedical insights.

Publications from HeartBD2K

See below for recent publications from our Center's investigators. For more information, see our page at