BioMedical Computing and Standards

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BioMedical Computing and Standards
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BioMedical Computing

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

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Designer Drugs
Pattern Recognizer
DB
Yay! Standards
DB
Microarray
Happy Patient thankful software engineering and
standards will make it possible
DB
Tissue Sample
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Challenges

• Extremely large Datasets
• Incompatible Data formats and languages
• Human Safety
• Collaboration Vs. Security

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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

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The Data
you
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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 )

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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

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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

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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

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Aspects of BioMedical Computing
This one could be collaborative
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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

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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

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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

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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

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Standards in Archiving

• HIPAA
• Requires you to protect stored datas
• Confidentiality
• Integrity
• Availability

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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

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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

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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

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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

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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

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Sequences
Data Dictionary
Data Mart
Medical Records
Medical Records
Data User
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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

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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

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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

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Time For Questions!