IC Applications Show & Tell Program

June 3, 2014


Contents Page Show Time
Introduction ......................................................................................................... 8:35
Publications Clearance System ......................................................................... 1 8:45
Biospecimen Research Database (BRD) ............................................................ 2 9:00
Comprehensive Data Resource (CDR) ............................................................... 3 9:15
Individual Development Plans (IDP) ................................................................. 4 9:30
Administrative Hub (One Stop Shop) ................................................................ 5 9:45
NIBIB Asset Management System .................................................................... 6 10:00
ChemCom: a Chemical Comparator ................................................................. 7 10:15
My Ethics ........................................................................................................... 8 10:30

Introduction
This event is the third quarterly Show & Tell event organized by the Enterprise Architecture program of
National Heart, Lung, and Blood Institutes Office of Management, IT and Applications Center (ITAC). We
have been pleased to create a forum for application users and technicians from across the NIH to share
technology that improves how our work is done, and we look forward to joining with partners from other
ICs to entrust this stewardship activity to a trans-NIH group for the future.
While every application may not interest everyone in the NIH, the willingness to share both technologies
and the stories behind them is essential for our collective success.
1
App Name: PUBLICATIONS CLEARANCE SYSTEM
Access URL: https://sps.nccam.nih.gov/ocpl/pcs
Docs URL: (if any) https://intranet.nccam.nih.gov/policies/clearance
IC: NCCAM
Submitter Name: Eric Gallagher
Email Address: Eric.Gallagher@nih.gov Phone 301-496-8258
Functional Area
Where Used:
Administrative How Acquired? Custom Development
App IT Contact: Sidhant Jain
Operating Sys: Windows Server 2008 R2 DBMS MS SQL Server 2008 R2
Front End: Microsoft SharePoint 2010
We intend to: Just an FYI / other
FUNCTIONALITY PROVIDED
The Publications Clearance System enables NCCAM staff to ensure that disseminated information is of
the highest quality, has been reviewed for substantive content, and has been administratively approved
by the appropriate Senior Staff. The PCS system tracks the request and routes it for approval. At each
stage of the process, NCCAM staff receives notifications. The notifications continue until the clearance
is complete.
NUMBER AND TYPE OF CURRENT USERS
About 50+. NCCAM POs, DIR staff, Senior Staff
EXTERNAL DATA USED
N/A
ADDITIONAL NOTES
[Type any additional notes if needed.]

2
App Name: BIOSPECIMEN RESEARCH DATABASE (BRD)
Access URL: http://biospecimens.cancer.gov/brd
Docs URL: (if any)
IC: NCI
Submitter Name: Ping Guan
Email Address: Ping.guan@nih.gov Phone (240) 276-5711
Functional Area
Where Used:
Extramural How Acquired? Custom Development
App IT Contact: Charles Shive (charles.shive@nih.gov, (301) 443-7068)
Operating Sys: PC, MAC compatible DBMS Oracle
Front End: Web-based GUI
We intend to: Provide this service to others
FUNCTIONALITY PROVIDED
The Biospecimen Research Database (BRD) is a free and publicly accessible database that contains
searchable summaries of peer-reviewed literature pertinent to the field of human biospecimen science.
The database is updated periodically with both recent and historical publications and serves as a vehicle
for literature review, evaluation of "in use" biospecimen handling protocols, development of new
protocols, and identification of analytes that are susceptible or impervious to handling variability. BRD
currently houses expertly curated summaries of 2035 published studies. BRD entries include primary
research or review articles that have been identified, reviewed, and curated by a Ph.D. level scientist.
For each paper contained within the BRD: (1) relevant parameters have been annotated, including the
biospecimen investigated (tissue/cell type, patient diagnosis), the preservation method employed, the
analyte of interest, and the technology platform applied; (2) relevant results have been summarized in
free-text fields; and (3) pre-analytical factors encountered during the lifecycle of a biospecimen (e.g.
ischemia time, fixation parameters, storage conditions) have been captured.
NUMBER AND TYPE OF CURRENT USERS
Curator: 3
Public User: Users are not individually tracked. In 2013 there was an average of 479 unique visitors per
month, and the site was accessed from 99 different countries. More recently, 308 unique visitors
located in 36 different countries accessed the BRD in March 2014.
EXTERNAL DATA USED
PubMed, numerous scientific journals.
ADDITIONAL NOTES
[Type any additional notes if needed.]


3

App Name: COMPREHENSIVE DATA RESOURCE (CDR)
Access URL: https://cahub.ncifcrf.gov (user account is required to access)
Docs URL: (if any)
IC: NCI
Submitter Name: Ping Guan
Email Address: Ping.guan@nih.gov Phone (240) 276-5711
Functional Area
Where Used:
Extramural How Acquired? Custom Development
App IT Contact: Charles Shive (charles.shive@nih.gov, (301) 443-7068)
Operating Sys: PC, MAC compatible DBMS Oracle
Front End: Web-based GUI
We intend to: Provide this service to others
FUNCTIONALITY PROVIDED
CDR is a distributed web-based system that manages and maintains multi-dimensional data models on
biospecimens. CDR was developed and is currently utilized to collect biospecimen and clinical data on
biospecimens collected from cancer patient donors and post-mortem donors, for the Biospecimen Pre-
analytical Variables (BPV) and Genotype-tissue Expression (GTEx) programs. As an efficient case
management tool capable of connecting to various remote informatics systems, CDR could be adopted
by the broader research community to standardize and streamline biobanking operations. CDR was
developed by the Frederick National Laboratory for Cancer Research (FNLCR) and is built with a
combination of open-source and commercial technologies including Grails, Oracle, Groovy, jQuery, and
Apache Solr.

CDR provides secure data access based on users roles and privileges. Through dynamic content
redaction, it protects private information in compliance with HIPPA regulations. Its graphic user
interfaces streamline data entry workflow based on SOPs for sample collection and processing. The
automated data checks and validations confirm data integrity and SOP adherence simultaneously. Web
services APIs allow NCI pathologists to access digital imaging data housed remotely at a separate
Comprehensive Biospecimen Resource (CBR). APIs connect to CBRs LIMS system for real-time sample
inventory. The reporting and analytics module supports data analysis and aggregation, report
generation and real-time operational data snapshots. The BPV and GTEx programs have their own entry
point at CDRs login page. BPV is designed to systematically investigate the effects of individual pre-
analytical variables on the molecular profiles of biospecimens. The program collects surgical tumor
samples under pre-defined pre-analytic conditions. The GTEx program studies gene expression and
regulation across multiple human tissues. GTEx aims to collect 25 ~30 different types of tissues from
approximately 900 healthy normal donors.
NUMBER AND TYPE OF CURRENT USERS: 174 total users as of April 2014. 47 NCI users (5 roles, including Read-
only, Pathologist, Data Manager, Limited Data Set Read-only, and Admin). 127 project users (spanning 8
biospecimen collection sites and 3 institutional collaborators).
EXTERNAL DATA USED: NCI Thesaurus, ICD10-CM, NLM Unified Medical Language System (UMLS), FDA
NDC, PDQ Disease List, AMAs Current Procedural Terminology (CPT).
ADDITIONAL NOTES: The CDR is hosted at the ABCC, FNLCR, and uses tri-mode authentication (NIH LDAP, local
4
user and machine accounts.) All web traffic is SSL encrypted.
App Name: INDIVIDUAL DEVELOPMENT PLANS (IDP)
Access URL: https://idp.nhlbi.nih.gov
Docs URL: (if any) https://intranet.nhlbi.nih.gov/general/individual-development-plan-idp (NHLBI
Intranet)

IC: NHLBI
Submitter Name: Kimberly Barone
Email Address: Kimberly.barone@nih.gov Phone 301-496-0861
Functional Area
Where Used:
Administrative How Acquired? Custom Development
App IT Contact: Matt Raschka
Operating Sys: Linux DBMS MySQL
Front End: PHP
We intend to: Share code as requested
FUNCTIONALITY PROVIDED
An Individual Development Plan (IDP) is a tailored action plan that details short and long-term goals for
an employees professional and career development and is mutually beneficial to both the employee
and the organization.
The IDP system is currently in a pilot phase in OM. The IDP portal allows participants to electronically
capture their plans, pull content from previously used IDPs, utilize existing populated suggested courses
for Supervisors and COR training, and have historical access to previous IDPs. Supervisors are able to
track their employees IDPs in one place.
The back-end reporting allows NHLBI to track developmental goals by organization and across NHLBI.
Allows to monitor completion of IDPs (can sort by date/organization/name/etc), and pull various
formats of reports. Reports assist in gathering training needs for the IC.
NUMBER AND TYPE OF CURRENT USERS
NHLBI OM Pilot, 79 approved plans, with 22 in a draft phase (draft/pending review/returned for
editing).
EXTERNAL DATA USED
Application pulls user data from NED
ADDITIONAL NOTES
We plan to expand the pilot in NHLBI (currently looking at rolling out to 1-2 more groups who have
expressed interest), and eventually to entire IC.

5
App Name: ADMINISTRATIVE HUB (ONE STOP SHOP)
Access URL: http://adminhub.nih.gov
Docs URL: (if any) N/A
IC: NIBIB, NIDA, and OD [Office of Strategic Planning for Administration (OSPA)]
Submitter Name: Martha Randazzo, OD/OM/OSPA
Email Address: randazzm@mail.nih.gov Phone 301-402-8698
Functional Area
Where Used:
Administrative How Acquired? Custom Development
App IT Contact: Zoe Ann Copeland, NIBIB, and Anuraj Dandgaval, NIBIB
Operating Sys: Windows server 2008/IIS 7.5
(Good to have Linux/Unix OS
and Apache hosting)
DBMS MySQL 5.1
Front End: HTML, CSS, Drupal 7, JavaScript/Jquery
We intend to: Just an FYI / other
FUNCTIONALITY PROVIDED
As part of the One Stop Shop (OSS) initiative, the Administrative Hub is an iterative, phased resource for
centrally locating links to authoritative administrative information and systems across various functional
areas for more efficient and effective administrative functions.
NUMBER AND TYPE OF CURRENT USERS
Since the Admin Hubs launch in January 2014, approximately 3000 people in the NIH administrative
community have accessed the site.
EXTERNAL DATA USED
N/A
Additional Notes
Following the retirement of the NIH Portal, the One Stop Shop (OSS) initiative team deployed the Admin
Hub as an early-phase resource to serve the informational needs of administrators with centralized
key links needed for day-to-day work.


6
App Name: NIBIB ASSET MANAGEMENT SYSTEM
Access URL: n/a
Docs URL: (if any) n/a
IC: NIBIB
Submitter Name: Anthony Dorrion
Email Address: Anthony.dorion@nih.gov Phone 240-383-6612
Functional Area
Where Used:
IT How Acquired? Custom Development
App IT Contact: Anthony Dorion
Operating Sys: Windows/Mac OSX/iOS DBMS Filmaker Pro 11
Front End: Filemaker Pro 11
We intend to: Share code as requested
Functionality Provided
The NIBIB Asset Management System is a database developed and designed to account and track all IT
equipment assigned to all NIBIB users. The database is a tool used to reconcile records between the IT
Staff, who receive and decal current and new property, and the Property Custodial team who update
and manage NIBIB property on the Administrative side. The Asset Management Systems was designed
to eliminate the error-prone, time-intensive manual process of property tracking and transfer and
automate the various tasks involved. Remote access to system via iPad/iPhone and Web Browser allow
it to be accessible from any location, securely. Since the system has been in production, Mid 2013, there
has been a significant reduction in errors and time due to the automated processes and functions.
Benefits to date include a 44% reduction on NIBIBs total shortage value, a 75% reduction in time spent
on adds/changes, and a near 85% reduction in time spent searching for property.

NUMBER AND TYPE OF CURRENT USERS
Management Staff: 7
IT Staff: 7

EXTERNAL DATA USED
SUNFLOWER

ADDITIONAL NOTES


7
App Name: CHEMCOM: A CHEMICAL COMPARATOR
Access URL: http://brbweb2.nci.nih.gov/~jwfang/ChemCom/launchJNLP.jnlp
Docs URL: (if any)
IC: NCI
Submitter Name: Jianwen Fang
Email Address: Jianwen.fang@nih.gov Phone 240-276-7672
Functional Area
Where Used:
Intramural How Acquired? Choose an item.
App IT Contact: Jianwen Fang
Operating Sys: All platforms supporting Java 7
and OpenBabel (Windows,
OSX, LINUX/UNIX, etc)
DBMS N/A
Front End: Java Web Start
We intend to: Just an FYI / other
FUNCTIONALITY PROVIDED
ChemCom provides an intuitive graphic interface to four algorithms for structure similarity based
searches and comparisons of chemical libraries. The fastest algorithm is more than 10 times faster than
the OpenBabel FastSearch.
NUMBER AND TYPE OF CURRENT USERS
HTS staff, computational chemists, and other people need to search and compare chemical libraries.
EXTERNAL DATA USED
None
ADDITIONAL NOTES
The program is currently a standalone application with a user-friendly graphic interface. But it can be
easily modified to a component of a large system to perform the specific functionalities.


8
App Name: MY ETHICS
Access URL: http://myethics.nibib.nih.gov/SitePages/Home.aspx
Docs URL: (if any) N/A
IC: NIBIB
Submitter Name: Kai Lakeman Management Analyst, NIBIB
Email Address: Kai.Lakeman@nih.gov Phone
301-594-9646
Functional Area
Where Used:
All Areas How Acquired? Custom Development
App IT Contact: Zoe-Ann Copeland, Deputy Executive Officer, NIBIB
Operating Sys: N/A DBMS N/A
Front End: SharePoint Foundation
We intend to: Provide this service to others
FUNCTIONALITY PROVIDED
This application serves as a tool to navigate the NIH Ethics Program, HHS/OGC and Office of
Government Ethics websites. It presents information to users in three formats 1) by Topic in a FAQ
manner 2) by Category and 3) by User type. A Glossary of terms is a unique feature designed to
increase knowledge and awareness of common ethics terms.
NUMBER AND TYPE OF CURRENT USERS
It is currently open to all NIH staff who have active directory accounts. Users external to NIH (potential
employees) may request access by submitting a help desk ticket. It has been demonstrated to 19 of the
27 IC Ethics Offices and to the Trans-NIH Management Analyst Working Group
EXTERNAL DATA USED
http://ethics.od.nih.gov/
http://intranet.hhs.gov/ethics/
http://www.oge.gov/home.aspx
ADDITIONAL NOTES
My Ethics is a RAD prototype, it is not 508 compliant. We are collecting feedback to develop a second
generation My Ethics which will incorporate the ability to track usage. It is hosted on a NIBIB SharePoint
server. Users have the ability to submit suggestions for additional content via an NIH help desk ticket.