BioMedical Computing and Standards - PowerPoint PPT Presentation

1 / 26
About This Presentation
Title:

BioMedical Computing and Standards

Description:

Medical equipment. Laboratory automation. Archiving. Public and Private Databases. Data Dictionary ... Medical Records. Data Mart. Medical Records. Data ... – PowerPoint PPT presentation

Number of Views:122
Avg rating:3.0/5.0
Slides: 27
Provided by: CSS6
Category:

less

Transcript and Presenter's Notes

Title: BioMedical Computing and Standards


1
BioMedical Computing and Standards
2
BioMedical Computing
  • Medical Equipment
  • Cellular and system simulation
  • Data mining for medical correlations
  • Determining Protein structures
  • Sequencing Genes
  • Personalized medicine ( the holy grail )

3
Designer Drugs
Pattern Recognizer
DB
Yay! Standards
DB
Microarray
Happy Patient thankful software engineering and
standards will make it possible
DB
Tissue Sample
4
Challenges
  • Extremely large Datasets
  • Incompatible Data formats and languages
  • Human Safety
  • Collaboration Vs. Security

5
Large Datasets
  • GenBank contains over 15 million sequence records
  • Many Bioinformatics companies have 200 terabyte
    storage for proprietary information
  • Most systems incorporate proprietary information
    with multiple sources of public information

6
The Data
you
7
Incompatible Data
  • Mesh ( medical subject heading )
  • UMLS ( unified medical language system )
  • RCS ( read classification system )
  • SNOMED ( systemized nomenclature of human and
    veterinary medicine )
  • ICD-ID ( international classification of diseases
    )
  • CPT ( current procedural terminology )
  • GEML ( gene expression markup language )
  • MAML ( microarray markup language )
  • FASTA ( popular sequence data format )
  • MmCIF( popular format for describing 3d
    structures )
  • and many more!!! ( especially proprietary ones )

8
Human Safety
  • Medical devices are LIFE CRITICAL
  • About 5000 compounds evaluated by pharmaceutical
    companies yearly, 5 make it to human trials, 1
    makes it to market
  • 4995 were thrown out right away
  • 4 were thrown out after they were tried on people
  • One of the major reasons is safety

9
Collaboration and Security
  • There WILL be attacks
  • BioMedical information can be worth a lot
  • There are active groups that appose certain
    BioMedical research areas
  • There are now laws regarding medical
    informations security and privacy
  • Security breaches can turn into lawsuits now
  • Collaboration is very high in BioMed

10
Aspects of BioMedical Computing
  • Process Control
  • Medical equipment
  • Laboratory automation
  • Archiving
  • Public and Private Databases
  • Data Dictionary
  • Backups
  • Numerical Processing
  • Simulations
  • Data mining
  • Visualization
  • Communications
  • Collaborative software
  • Software that facilitates collaboration

11
Aspects of BioMedical Computing
This one could be collaborative
12
Aspects of BioMedical Computing
  • The four aspects are usually combined in one way
    or another to make one BioMedical tool or system
  • Chimera combines collaboration and modeling
  • Entrez combines archiving and numerical analysis

13
Importance of Standards
  • Capture best practices
  • Reuse of what works helps prevent mistakes from
    being repeated and helped success be duplicated
  • Help increase safety, and are often required in
    life critical systems
  • Can be a helpful marketing tool, who wants to by
    a noncompliant produce?
  • Maintenance and re-engineering is easier if
    program was designed and coded using documented
    standards

14
Standards in Process Control
  • IEEE 1073 family of standards
  • Point of care medical device communications
    standards
  • Specify formats, speeds, and communication
    protocols for medical devices
  • Goal is standardized plug and play medical
    equipment
  • Covers devices such as vital signs monitors,
    defibulators, weighing scales, and much much more
  • Aims to increase safety by allowing devices to
    interact, increasing continuity of care
  • Are a work in progress

15
Standards in Archiving
  • HIPAA
  • Health insurance portability and accountability
    act
  • Its not just another pretty acronym, its the
    law
  • HIPAA covers
  • Health plans, Health clearinghouses, and
    healthcare providers
  • Entities with business relations with a covered
    entity
  • Contractors, consultants, and service providers
  • Paid researchers
  • Anonymous information is not covered

16
Standards in Archiving
  • HIPAA
  • Requires you to protect stored datas
  • Confidentiality
  • Integrity
  • Availability

17
Standards in Archiving
  • HIPAA
  • HIPAA requires that standards are in place, but
    is open ended
  • The Process HIPAA recommends for implementing
    security standards is
  • Assess risks and vulnerabilities to information
  • Develop, implement and maintain security measures
    appropriate to your particular needs
  • Document these measures in the form of standards

18
Standards in Archiving
  • HIPAA
  • HIPAA does have some more specific requirements
    with regard to security of archiving
  • The standards shall include access control
  • The standards shall include some form of crypto
  • The standards shall include a data backup plan
  • The standards shall include a disaster recovery
    plan
  • The standards shall include and emergency
    operation plan
  • The standards shall be periodically reviewed and
    tested, and the timetable for this shall be in
    the standards

19
Standards in Archiving
  • HIPAA
  • HIPAA standards are mostly operating procedure
    standards, but can still impact software design
    considerably
  • When designing software for medical entities
  • When maintaining and re-engineering systems that
    are not compliant
  • When making BioMedical software that must use
    data owned by covered entity

20
Standards in Archiving
  • Data Dictionary
  • BioMedical programs must often access numerous
    public databases
  • GenBank ( for gene sequences )
  • SwisProt ( for protein sequences )
  • PDB ( for 3d protein structures )
  • Even databases that contain the same type of info
    often have different data formats
  • Companies and programs need to tie these
    different databases with different formats into
    one consistent data mart for utilization
  • This is achieved with a standard Data Dictionary

21
Standards in Archiving
  • Data Dictionary
  • A Data Dictionary must contain one standard
    format for all types of information to be
    integrated
  • A Data Dictionary must contain standards on how
    to convert other formats that will be accessed
    into the standard format

22
Sequences
Data Dictionary
Data Mart
Medical Records
Medical Records
Data User
23
Standards in Numerical Processing
  • Data Mining makes use of the Data Dictionary
  • Visualization makes use of standard look and
    feel that users are accustomed to
  • OpenGL is the de facto standard for implementing
    3D graphics in BioMedical computing

24
Standards in Communications
  • HIPAA
  • HIPAA requires data transfer systems to have
    standards that address the following
  • Data Integrity
  • Message Authentication
  • Entity authentication
  • Access Controls
  • Encryption
  • Alarms
  • Audit trails
  • Event reporting

25
Conclusions
  • BioMedical Computing faces many challenges and
    risks
  • Large and Incompatible data sets
  • Human safety
  • Collaboration vs. security
  • These challenges and risks are met with the use
    of standards

26
Time For Questions!
Write a Comment
User Comments (0)
About PowerShow.com