# Computational Support for All Echinobase Objectives

> **NIH NIH P41** · CARNEGIE-MELLON UNIVERSITY · 2021 · $154,311

## Abstract

Computational Component 1: Computational Support for all Echinobase Objectives
SUMMARY
Echinobase is the only centralized and curated repository of genomic features for multiple species of
echinoderms. The primary mode of access to Echinobase resources is through a web information system that
displays content stored in annotation databases as useful and informative web pages and applications. This
requires maintaining data and applications in a secure, high performance, web-accessible environment and
ensuring that this system remains at peak performance through regular upgrading and maintenance of all
software and hardware. This component addresses these needs by implementing a system build from a clone
of Xenbase, the Xenopus model organism database. Through this approach Echinobase will acquire the
database with a customized Chado schema, a java based web app, and various other tools developed and
optimized by Xenbase personnel. In particular Echinobase will acquire a searchable gene expression database,
and highly automated curation pipelines. Automated pipelines will be customized to load and contain
echinoderm-specific data (i.e. genomes, transcriptomes, annotations, etc). The website frontend will be
modified to project a unique Echinobase user interface that supports the unique features of Echinobase and its
users preferences. Thus, through this proposal, Echinobase leverages more than 10 years and $8 million of
Xenbase development and expertise. This provides an extensive improvement in functionality for Echinobase
at a fraction of the cost of providing updates in isolation. This innovative and cost saving approach supports
both expanded functionalities of Echinobase (i.e. the addition of a gene expression database) as well as
broader initiatives of database coalescence. Computational support will be provided for the deployment of
BioTapestry, a gene regulatory network modeling and viewing software addition proposed to integrate with
Echinobase. This component will also provide critical support the data, curation, and software innovations from
the other components of this application; it is the backbone of the entirety of Echinobase.

## Key facts

- **NIH application ID:** 10241293
- **Project number:** 5P41HD095831-04
- **Recipient organization:** CARNEGIE-MELLON UNIVERSITY
- **Principal Investigator:** PETER D VIZE
- **Activity code:** P41 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $154,311
- **Award type:** 5
- **Project period:** 2018-09-20 → 2023-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10241293

## Citation

> US National Institutes of Health, RePORTER application 10241293, Computational Support for All Echinobase Objectives (5P41HD095831-04). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10241293. Licensed CC0.

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