Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

High-performance implementation and analysis of the Linkmap program.

K Kothari1, N Lopez-Benitez, S E Poduslo

  • 1Computer Science Department, Texas Tech University, Lubbock, Texas 79409, USA.

Journal of Biomedical Informatics
|August 30, 2002
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Four major phosphoproteins and active phosphatidylinositol turnover in oligodendroglial plasma membranes.

Neurochemistry international·2010
Same author

Ketone bodies as precursors for lipid synthesis in neurons, astrocytes, and oligodendroglia (myelin) in hyperthyroidism, hyperketonemia and hypoketonemia.

Neurochemistry international·2010
Same author

Ketone body enzyme activities in purified neurons, astrocytes and oligodendroglia.

Neurochemistry international·2010
Same author

A sensitive immunotransfer method for the detection of oligodendroglial plasma membrane antigens.

Neurochemistry international·2010
Same author

Laparoscopic salvage total pelvic exenteration: Is it possible post-chemo-radiotherapy?

Journal of minimal access surgery·2010
Same author

Maintenance of bulk isolated neurons.

Neuroscience letters·2009
Same journal

CoAff-DTI: Fine-grained drug-target interaction prediction using pre-trained language models and affinity-guided mechanisms.

Journal of biomedical informatics·2026
Same journal

Evaluation of temporal preservation in synthetic longitudinal patient data.

Journal of biomedical informatics·2026
Same journal

ARKE: An ontology-driven framework for automated mapping of local radiology procedure terms to the LOINC-RadLex playbook using large language model.

Journal of biomedical informatics·2026
Same journal

A validation-driven training controller for cross-lingual biomedical NER via reinforcement learning-based adaptive loss weighting.

Journal of biomedical informatics·2026
Same journal

ASP-HR: An Adaptive Spatial Perception and Hierarchical Reasoning mechanism for document-level biomedical relation extraction.

Journal of biomedical informatics·2026
Same journal

Beyond Accuracy: Safety-Centered guidelines for the evaluation of LLM-based therapy recommendation systems for chronic multimorbidity patients.

Journal of biomedical informatics·2026
See all related articles

This study parallelized the Linkmap program for faster genetic linkage analysis using a dynamic master-slave scheme on a high-performance cluster. This significantly speeds up complex gene mapping calculations for medical research.

Area of Science:

  • Computational Biology
  • Genetics
  • High-Performance Computing

Background:

  • Genetic linkage analysis, crucial for mapping genes and identifying disease genes, relies on family pedigree data.
  • Estimating the recombination fraction (theta) between loci is computationally intensive, especially for large pedigrees and numerous markers.

Purpose of the Study:

  • To implement a dynamic master-slave parallelization scheme for the Linkmap program.
  • To accelerate genetic linkage calculations on a high-performance computing cluster (Origin 2000).
  • To evaluate the performance of the parallelized Linkmap program.

Main Methods:

  • Developed and implemented a dynamic master-slave parallelization strategy.
  • Applied the scheme to the Linkmap program, a component of the widely used LINKAGE/FASTLINK package.

Related Experiment Videos

  • Utilized a high-performance cluster with 56 R12000 processors (Origin 2000).

    • Main Results:

    • Successfully parallelized the Linkmap program, demonstrating significant computational speedup.
    • Compared performance against previous implementations on DEC Alphas and sequential execution on the O2K.
    • Addressed implementation challenges associated with parallelizing genetic linkage analysis software.

    Conclusions:

    • The dynamic master-slave parallelization scheme is effective for accelerating Linkmap computations.
    • This approach enhances the feasibility of genetic linkage analysis for large-scale genetic studies.
    • Optimized computational methods are vital for advancing gene mapping and disease gene discovery.