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Services: Case Studies |
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Codes to the left of the case study description correspond to the types of services we offer.
- PM-- Project Management
- DB-- Data Management and Databases
- QA-- Quality
- SE-- Embedded/ Scientific Programming
For case studies related to our product, bioinstrument Manager,
go to
Products Case Studies.
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Case Study Descriptions |
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PM
DB
QA
SE |
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Test for alcohol-related diseases for the NIH
The National Institute on Alcohol Abuse
and Alcoholism (http://www.niaaa.nih.gov),
part of the National Institutes of Health (
http://www.nih.gov/),
needed to detect the state of alcohol-related diseases in
organs. The challenge was to use a cost effective, efficient
process with more scientific rigor than the current Web-based patient
self-evaluation survey for alcohol disease screening. Through funding
from an NIH Small Business Innovation Research (SBIR) grant,
Userspace developed a prototype solution to quantify immune
precursor pathways using small molecule lipids. As a result,
scientists can…
- Use samples from dose/response animal studies to identify
potential biomarkers.
- Run extracted blood plasma samples through LC columns in less than 3
minutes.
A portion of this research was paid
through a Small Business Innovation Research (SBIR) grant from the
National Institutes of Health (
http://www.nih.gov/).
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PM
DB
QA
SE |
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Near Real-time proteomics analysis for the NIH
The National Institute on Alcohol Abuse
and Alcoholism (
http://www.niaaa.nih.gov/), part of the National Institutes of Health (
http://www.nih.gov/),
needed to analyze reams of mass spectrometry data in process instead
of after a run's completion. The challenge was to use a cost effective, efficient
process that allowed End Users to halt an ineffective process and save samples and consumables.
Through funding from an NIH Small Business Innovation Research (SBIR) grant,
Userspace developed a prototype router to process data in real-time. As a result,
scientists can…
- Use an instrument protocol computer cluster built by Userspace to manage
ultra-low flow and peak parking methods.
- Store the instrument process protocol in XML and the data format in mzXML.
- Analyze MS data in near real-time with a data analysis computer cluster.
- Use a multidimensional mass spectrometry analysis toolkit to analyze and
archive large datasets.
- Manage the process and the data using the BioInstrument Manager platform.
A portion of this research was paid
through a Small Business Innovation Research (SBIR) grant from the
National Institutes of Health (
http://www.nih.gov/).
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PM
QA
SE |
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Multidimensional flow cytometry data analysis and reporting
Physician
experts at HematoLogics, Inc. (
http://www.hematologics.com)
needed to provide early prognosis for leukemia using small cell
populations and flow cytometry specimen analysis. The challenge
was using the same sample preparation, separation and introduction
techniques for flow cytometry and providing the same high degree of
accuracy but with a very small population (100) of bad cells within a
population of 200,000 cells. Userspace’s solution was to
develop a 7-dimensional analysis tool and algorithm to process and
display data points graphically. The results are HematoLogics’
physicians can use the tool to…
- Select cell characteristics for analysis.
- Assign axes for graphing and display.
- Rotate the graph in spherical space.
- Export the graphs to JPEG format.
A portion of this research on Multi-Dimensional Flow Cytometry was paid
through a Small Business Innovation Research (SBIR) grant from the
National Cancer Institute (
http://www.nci.nih.gov/).
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SE |
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2D computer-based manipulation of robotics
The Biochemistry Department at the
University of Washington (
http://depts.washington.edu/biowww/) needed to efficiently and consistently manipulate fragile,
expensive crystals to evaluate their 3-dimensional structure using an
X-Ray Defraction (XRD) platform. The challenge was to center
the crystal in front of the XRD without human physical intervention.
Userspace’s solution was to develop software that
automatically centered the crystal on a 6-axis plane in 2D space in
front of the XRD using image-guided robotic algorithms. The results
are lab personnel can…
- Use a Sony Industrial Camera with a microscope lens and 2D monitor to
position the crystal along six (6) axes.
- Click on the 2D screen to instruct the robotic arm where to place the
crystal in 3D space.
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PM
SE |
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64-bit computer cluster for protein and peptide sequencing
The Mass Spectrometry Lab in the
Medicinal Chemistry Department at the University of Washington
(
http://depts.washington.edu/medchem/) needed to reduce the cost for sequencing proteins.
The challenge was to increase the sequencing speed, reduce the processing time and
maintain accuracy while keeping the overall cost within budget.
Userspace’s solution was to build a 12-node, 64-bit
computer cluster for protein/peptide sequencing and
compile/install/configure open source software. The results
are MS personnel and researchers can…
- Reduce the sequencing of proteins from two (2) days to 4-6 hours depending
on the complexity of the proteins.
- Use a compact, high-end distributed cluster of data servers and
processing nodes.
- Operate a compilation of reputable but disparate open source programs as a
single analysis platform (Protein Prophet, Peptide Prophet, ProbID,
EXPRESS and ASAP Ratio, now part of the Trans-Proteomic Pipeline).
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PM |
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Business Process Analysis in an FDA-regulated company
An FDA-regulated company
needed to document the business processes for a program redesign. The challenge
was to include 21 CFR Part 11 and PDMA validation components within the company and between the company, its vendors and
its fulfillment partners. Userspace’s solution was to use ProVision to model the business and workflow processes.
The results are Program Managers, developers and Quality Control can…
- Drill down multiple levels to see enough detail to satisfy
development, documentation and validation.
- Incorporate the JPEG images into QC documentation.
- See how standard operating procedures integrate into
the overall business processes.
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PM
DB
QA |
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Engineering Validation in an FDA-regulated company
An FDA-regulated company
needed to validate a program redesign and deployment for their company's backbone product. The challenge
was to include 21 CFR Part 11 and PDMA validation components within the company and between the company, its vendors and
its fulfillment partners. Userspace’s solution was to provide quality assurance planning and documentation
for system architecture, data integrity and conversion and security.
The results are Program Managers, developers and Quality Control can…
- Work from a complete, compliant set of requirements.
- Develop Quality Assurance processes.
- Deploy a validated system.
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PM
DB
QA
SE |
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Reverse engineering secure databases
A security firm
needed to gain access to various data compiled in a variety of formats. The challenge
was to extract the data from unknown formats. Userspace’s solution was to research tools for data extraction and
develop programmatic solutions for extracting compiled Java code databases.
The results are the client can…
- See a proposed data model of the extracted data.
- Use the extracted data in CSV format.
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