BioMedical Computing and Standards

BioMedical Computing• Medical Equipment

• Cellular and system simulation

• Data mining for medical correlations

• Determining Protein structures

• Sequencing Genes

• Personalized medicine ( the holy grail )

Yay! Standards

DB

DB

DB

Pattern Recognizer

Microarray

Tissue Sample

Designer Drugs

Happy Patient thankful software engineering and standards will make it possible

Challenges• Extremely large Datasets

• Incompatible Data formats and languages

• Human Safety

• Collaboration Vs. Security

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

you

The Data

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 )

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

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 information’s security and privacy – Security breaches can turn into lawsuits now

• Collaboration is very high in BioMed

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

Aspects of BioMedical Computing

This one could be collaborative

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

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

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

Standards in Archiving • HIPAA

– Health insurance portability and accountability act

– It’s not just another pretty acronym, it’s 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

Standards in Archiving • HIPAA

– Requires you to protect stored data’s • Confidentiality• Integrity• Availability

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

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

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

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”

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

Sequences

Medical Records

Data Mart

Medical Records

Data

Dictionary

Data User

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

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

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

Time For Questions!