2d:null 2e:["$","title",null,{"children":"BrazWebinar | Jonas Almeida | Observable"}] 33:T8c2,### Key Manuscripts: * *Praphulla MS Bhawsar, Mustapha Abubakar, Marjanka K Schmidt, Nicola J Camp, Melissa H. Cessna, Máire A Duggan, Montserrat García-Closas, Jonas S Almeida (2021) Browser-based Data Annotation, Active Learning and Real-Time Distribution of AI Models: From Tumor Tissue MicroArrays to COVID-19 Radiology. **J Pathology Informatics (in press)** * * *Almeida JS, M Shiels, P Bhawsar, B Patel, E Nemeth, R Moffitt, M Garcia Closas, N Freedman, A Berrington (2020) Mortality tracker - the COVID-19 case for real time web APIs as epidemiology commons. J Bioinformatics [**PMID:33135727**]. * * *Erich Bremer, Joel Saltz, and Jonas Almeida (2020) ImageBox2 - efficient and rapid access of image tiles from whole slide images (WSI) using Serverless HTTP range requests. J Pathol Inform Sep 10;11:29. [**PMID:33163255**].* * *Han Le, Rajarsi Gupta, Le Hou, Shahira Abousamra, Danielle Fassler, Luke Torre-Healy, Richard A Moffitt, Tahsin Kurc, Dimitris Samaras, Rebecca Batiste, Tianhao Zhao, Arvind Rao, Alison L Van Dyke, Ashish Sharma, Erich Bremer, Jonas S Almeida, Joel Saltz (2020) Utilizing Automated Breast Cancer Detection to Identify Spatial Distributions of Tumor-Infiltrating Lymphocytes in Invasive Breast Cancer. Am J. Pathol. (20)30188-7. [**PMID:32277893**].* * *Almeida JS, Hajagos J, Saltz J, Saltz M. 2019. Serverless OpenHealth at data commons scale—traversing the 20 million patient records of New York’s SPARCS dataset in real-time. PeerJ 7:e6230 [**PMID:30671301**].* * *Wilkinson S, JS Almeida (2014) QMachine: commodity supercomputing in web browsers. BMC Bioinformatics [**PMID:24913605**]. * * *Almeida JS, A Grüneberg, W Maass, S Vinga (2012) Fractal MapReduce decomposition of sequence alignment. Algorithms for Molecular Biology 7:12 [**PMID:22551205**]* 34:T40a,

Thank You

To the many wonderful collaborators (co-authors above) at the groups led by ...

NCI / DCEG - Montserrat García-Closas

SUNY / Stony Brook - Joel Saltz

and to NCI's Academic partnership program funding the data science graduate research of

Praful Bhawsar.

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BrazWebinar

\nJonas Almeida @ Brazilian Webinars on Bioinformatics, LNCC.br, July 23, 2021.\n
\n","pinned":false,"hidden":false,"mode":"html","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":43,"value":"bit.ly/brazwebinar","pinned":false,"hidden":false,"mode":"html","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":440,"value":"

","pinned":false,"hidden":false,"mode":"html","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":27,"value":"$33","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":90,"value":"

Why a reactive notebook instead of slides?

\nTo demonstrate the zero footprint FAIR cancer data commons it entails.","pinned":false,"hidden":false,"mode":"html","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":112,"value":"* *Wilkinson et. al (2016). The FAIR Guiding Principles for scientific data management and stewardship. Sci Data 3:160018. doi: 10.1038/sdata.2016.18. [**PMID: 26978244**].*\n\n* *Perkel JM. Reactive, reproducible, collaborative: computational notebooks evolve. Nature. 2021 May;593(7857):156-157. doi: 10.1038/d41586-021-01174-w. [**PMID: 33941927**].*\n ","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":472,"value":"## FAIR spaces\n\nExamples the data owners themselves enable (the **R** in FAIR) \n\n * The Cancer Genome Atlas (TCGA): bit.ly/tcgascope.\n * Discharge patient records in NY: bit.ly/loadsparcs.\n * Suffolk county, Long Island: bit.ly/pqiSuffolk.\n * point to another job, like dsrip ...\n * Mortality Tracker: https://episphere.github.io/mortalitytracker\n * Corona: https://observablehq.com/@episphere/corona \n * and conclude by twitting.\n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":571,"value":"### Fetch your own\n...","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":576,"value":"gm = (\n await fetch(\n \"https://health.data.ny.gov/resource/22g3-z7e7.json?hospital_county=Manhattan&ccs_diagnosis_description=Cancer%20of%20brain%20and%20nervous%20system&facility_name=Memorial%20Sloan%20Kettering%20Memorial%20Hospital\"\n )\n).json()","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":70,"value":"

Annotator-facing active AI annotation

","pinned":false,"hidden":false,"mode":"html","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":79,"value":"http://bit.ly/tcgatil","pinned":false,"hidden":false,"mode":"html","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":86,"value":"FileAttachment(\"tilmaps.png\").image()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":95,"value":"