SIMON: Open-Source Knowledge Discovery Platform

Overview

Journal Patterns (N Y)

Date 2021 Jan 29

PMID 33511368

Citations 9

Authors

Adriana Tomic

Ivan Tomic

Levi Waldron

Ludwig Geistlinger

Max Kuhn

Rachel L Spreng

Lindsay C Dahora

Kelly E Seaton

Georgia Tomaras

Jennifer Hill

Niharika A Duggal

Ross D Pollock

Norman R Lazarus

Stephen D R Harridge

Janet M Lord

Purvesh Khatri

Andrew J Pollard

Mark M Davis

Affiliations

Soon will be listed here.

Abstract

Data analysis and knowledge discovery has become more and more important in biology and medicine with the increasing complexity of biological datasets, but the necessarily sophisticated programming skills and in-depth understanding of algorithms needed pose barriers to most biologists and clinicians to perform such research. We have developed a modular open-source software, SIMON, to facilitate the application of 180+ state-of-the-art machine-learning algorithms to high-dimensional biomedical data. With an easy-to-use graphical user interface, standardized pipelines, and automated approach for machine learning and other statistical analysis methods, SIMON helps to identify optimal algorithms and provides a resource that empowers non-technical and technical researchers to identify crucial patterns in biomedical data.

Citing Articles

Integrative Mapping of Pre-existing Immune Landscapes for Vaccine Response Prediction.

Hao S, Tomic I, Lindsey B, Jagne Y, Hoschler K, Meijer A bioRxiv. 2025; .

PMID: 39896552 PMC: 11785181. DOI: 10.1101/2025.01.22.634302.

GeM-LR: Discovering predictive biomarkers for small datasets in vaccine studies.

Lin L, Spreng R, Seaton K, Dennison S, Dahora L, Schuster D PLoS Comput Biol. 2024; 20(11):e1012581.

PMID: 39541411 PMC: 11594404. DOI: 10.1371/journal.pcbi.1012581.

Obesity differs from diabetes mellitus in antibody and T-cell responses post-COVID-19 recovery.

Ali M, Longet S, Neale I, Rongkard P, Chowdhury F, Hill J Clin Exp Immunol. 2024; 218(1):78-92.

PMID: 38642547 PMC: 11404124. DOI: 10.1093/cei/uxae030.

Robustness and reproducibility for AI learning in biomedical sciences: RENOIR.

Barberis A, Aerts H, Buffa F Sci Rep. 2024; 14(1):1933.

PMID: 38253545 PMC: 10810363. DOI: 10.1038/s41598-024-51381-4.

Omicron infection following vaccination enhances a broad spectrum of immune responses dependent on infection history.

Hornsby H, Nicols A, Longet S, Liu C, Tomic A, Angyal A Nat Commun. 2023; 14(1):5065.

PMID: 37604803 PMC: 10442364. DOI: 10.1038/s41467-023-40592-4.

References

Pasolli E, Schiffer L, Manghi P, Renson A, Obenchain V, Truong D . Accessible, curated metagenomic data through ExperimentHub. Nat Methods. 2017; 14(11):1023-1024. PMC: 5862039. DOI: 10.1038/nmeth.4468. View

Warsinske H, Rao A, Moreira F, Santos P, Liu A, Scott M . Assessment of Validity of a Blood-Based 3-Gene Signature Score for Progression and Diagnosis of Tuberculosis, Disease Severity, and Treatment Response. JAMA Netw Open. 2019; 1(6):e183779. PMC: 6324428. DOI: 10.1001/jamanetworkopen.2018.3779. View

Horowitz A, Strauss-Albee D, Leipold M, Kubo J, Nemat-Gorgani N, Dogan O . Genetic and environmental determinants of human NK cell diversity revealed by mass cytometry. Sci Transl Med. 2013; 5(208):208ra145. PMC: 3918221. DOI: 10.1126/scitranslmed.3006702. View

Kourou K, Exarchos T, Exarchos K, Karamouzis M, Fotiadis D . Machine learning applications in cancer prognosis and prediction. Comput Struct Biotechnol J. 2015; 13:8-17. PMC: 4348437. DOI: 10.1016/j.csbj.2014.11.005. View

Sippy R, Farrell D, Lichtenstein D, Nightingale R, Harris M, Toth J . Severity Index for Suspected Arbovirus (SISA): Machine learning for accurate prediction of hospitalization in subjects suspected of arboviral infection. PLoS Negl Trop Dis. 2020; 14(2):e0007969. PMC: 7046343. DOI: 10.1371/journal.pntd.0007969. View

Libbrecht M, Noble W . Machine learning applications in genetics and genomics. Nat Rev Genet. 2015; 16(6):321-32. PMC: 5204302. DOI: 10.1038/nrg3920. View

Newell E, Sigal N, Bendall S, Nolan G, Davis M . Cytometry by time-of-flight shows combinatorial cytokine expression and virus-specific cell niches within a continuum of CD8+ T cell phenotypes. Immunity. 2012; 36(1):142-52. PMC: 3752833. DOI: 10.1016/j.immuni.2012.01.002. View

Robinson M, Sweeney T, Barouch-Bentov R, Sahoo M, Kalesinskas L, Vallania F . A 20-Gene Set Predictive of Progression to Severe Dengue. Cell Rep. 2019; 26(5):1104-1111.e4. PMC: 6352713. DOI: 10.1016/j.celrep.2019.01.033. View

Zeller G, Tap J, Voigt A, Sunagawa S, Kultima J, Costea P . Potential of fecal microbiota for early-stage detection of colorectal cancer. Mol Syst Biol. 2014; 10:766. PMC: 4299606. DOI: 10.15252/msb.20145645. View

10.

Chaudhury S, Duncan E, Atre T, Dutta S, Spring M, Leitner W . Combining immunoprofiling with machine learning to assess the effects of adjuvant formulation on human vaccine-induced immunity. Hum Vaccin Immunother. 2019; 16(2):400-411. PMC: 7062453. DOI: 10.1080/21645515.2019.1654807. View

11.

Lin H, Ray S, Tongchusak S, Reinherz E, Brusic V . Evaluation of MHC class I peptide binding prediction servers: applications for vaccine research. BMC Immunol. 2008; 9:8. PMC: 2323361. DOI: 10.1186/1471-2172-9-8. View

12.

Vamathevan J, Clark D, Czodrowski P, Dunham I, Ferran E, Lee G . Applications of machine learning in drug discovery and development. Nat Rev Drug Discov. 2019; 18(6):463-477. PMC: 6552674. DOI: 10.1038/s41573-019-0024-5. View

13.

Sweeney T, Perumal T, Henao R, Nichols M, Howrylak J, Choi A . A community approach to mortality prediction in sepsis via gene expression analysis. Nat Commun. 2018; 9(1):694. PMC: 5814463. DOI: 10.1038/s41467-018-03078-2. View

14.

Bonetta R, Valentino G . Machine learning techniques for protein function prediction. Proteins. 2019; 88(3):397-413. DOI: 10.1002/prot.25832. View

15.

Yip K, Cheng C, Gerstein M . Machine learning and genome annotation: a match meant to be?. Genome Biol. 2013; 14(5):205. PMC: 4053789. DOI: 10.1186/gb-2013-14-5-205. View

16.

Gregori G, Patsekin V, Rajwa B, Jones J, Ragheb K, Holdman C . Hyperspectral cytometry at the single-cell level using a 32-channel photodetector. Cytometry A. 2011; 81(1):35-44. DOI: 10.1002/cyto.a.21120. View

17.

Duggal N, Pollock R, Lazarus N, Harridge S, Lord J . Major features of immunesenescence, including reduced thymic output, are ameliorated by high levels of physical activity in adulthood. Aging Cell. 2018; 17(2). PMC: 5847865. DOI: 10.1111/acel.12750. View

18.

Deo R . Machine Learning in Medicine. Circulation. 2015; 132(20):1920-30. PMC: 5831252. DOI: 10.1161/CIRCULATIONAHA.115.001593. View

19.

Nolan J, Condello D . Spectral flow cytometry. Curr Protoc Cytom. 2013; Chapter 1:1.27.1-1.27.13. PMC: 3556726. DOI: 10.1002/0471142956.cy0127s63. View

20.

Bandura D, Baranov V, Ornatsky O, Antonov A, Kinach R, Lou X . Mass cytometry: technique for real time single cell multitarget immunoassay based on inductively coupled plasma time-of-flight mass spectrometry. Anal Chem. 2009; 81(16):6813-22. DOI: 10.1021/ac901049w. View