CIIPro is an online cheminformatics portal for large-scale chemical data analysis. It contains two main components: CIIProfiler, which creates an optimized biological profile for compounds based on their activities in assays, and CIIP Nearest Neighbor (BioNN), which uses the biological profile to calculate biological similarity and identify biological nearest neighbors to predict activity. CIIPro aims to integrate high-throughput screening data from sources like ToxCast and Tox21 with traditional toxicity data to improve in vitro to in vivo correlation and toxicity prediction models.
The document summarizes a 2-day conference on qPCR and digital PCR taking place on July 11-12, 2016 in Philadelphia. Over 150 industry and academic experts will discuss the latest developments and applications of qPCR and dPCR across various fields such as healthcare, plant science, food science and environmental testing. The conference will feature keynote speakers, case study presentations, a poster session and interactive panels on topics including digital PCR applications, qPCR strategies, healthcare case studies, and plant/food/environmental case studies. Confirmed speakers include experts from academic institutions and companies.
Presentation at the Canadian Cancer Research Conference satellite bioinformatics.ca workshop. This one is an introduction to tcga, icgc and cosmic databases.
Introduction - OECD Seminar on Bioinformatics and Regulation of Microbial Pes...OECD Environment
24 June 2019: This OECD seminar presented and discussed the potential use of genome sequence, bioinformatic tools and databases in a regulatory decision process for microbial pesticides.
Cancer genome databases & Ecological databases Waliullah Wali
Introduction
Biological databases are libraries of life sciences information, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis.
Information contained in biological databases includes gene function, structure, localization, clinical effects of mutations as well as similarities of biological sequences and structures.
Cancer genome databases
COSMIC cancer database
COSMIC cancer database
COSMIC is an online database of somatically acquired mutations found in human cancer.
The database is freely available.
COSMIC cancer database
Types of data
Expert curation data
Genome-wide screen data
COSMIC cancer database
Expert curation data
Manually input by COSMIC expert curators.
Consists of comprehensive literature curation followed by subsequent updates.
Includes additional data points relevant to each disease and publication.
Provides accurate frequency data as mutation negative samples are specified.
COSMIC cancer database
Genome-wide screen data
Uploaded from publications reporting large scale genome screening data or imported from other databases such as TCGA and ICGC.
Provides unbiased molecular profiling of diseases while covering the whole genome.
Provides objective frequency data by interpreting non mutant genes across each genome.
Facilitates finding novel driver genes in cancer.
Enter into -
COSMIC cancer database
by typing http://cancer.sanger.ac.uk/cosmic
in the address bar of Browser
Searching Process
Examples
Examples
Examples
Examples
Ecological databases
Ecological databases
Ecological databases is a source for finding ecological datasets and quickly figuring out the best ways to use them.
BioOne
DataONE
GEOBASE
BioOne
BioOne is a nonprofit publisher that aims to make scientific research more accessible.
BioOne was established in 1999 in Washington, DC.
BioOne is Complete and open-access.
It serves a community of over 140 society and institutional publishers, 4,000 accessing institutions, and millions of researchers worldwide.
Enter into -
BioOne Ecological database
by typing http://www.bioone.org/
in the address bar of Browser
How bioinformatic and sequencing data might inform the regulatory process - O...OECD Environment
24 June 2019: This OECD seminar presented and discussed the potential use of genome sequence, bioinformatic tools and databases in a regulatory decision process for microbial pesticides.
How can Whole Genome Sequencing information be used to address data requireme...OECD Environment
This document discusses the potential use of whole genome sequencing data to address regulatory requirements for approval of microorganisms as active ingredients in plant protection products in the EU. It analyzes how genome sequencing could be used for species assignment, relationship to pathogens, distinction between Bacillus strains, production of metabolites, antibiotic resistance, genetic stability, risk assessment, and unequivocal identification of strains. While noting some potential benefits, it also describes limitations and problems with relying solely on genome sequencing data. It concludes that genome sequencing can be useful to exclude some issues but should not be a standard requirement, and that only reports on analyses—not the genome sequences themselves—should be included in dossiers.
CIIPro is an online cheminformatics portal for large-scale chemical data analysis. It contains two main components: CIIProfiler, which creates an optimized biological profile for compounds based on their activities in assays, and CIIP Nearest Neighbor (BioNN), which uses the biological profile to calculate biological similarity and identify biological nearest neighbors to predict activity. CIIPro aims to integrate in vitro high-throughput screening data with in vivo toxicity information to help identify potential toxicants and develop robust toxicity models.
CIIProCluster: Developing Read-Across Predictive Toxicity Models Using Big DataDaniel Russo
This document summarizes the CIIProCluster approach for developing predictive toxicity models using large biological and chemical data. It clusters bioassays based on the chemical substructures that activate them to identify mechanisms of toxicity. For oral acute toxicity data, it extracts biological assay profiles for compounds and clusters 1,948 assays based on relevant fingerprints. Evaluation of a cluster of cytotoxicity assays shows their potential for predicting oral toxicity when restricting predictions to those with high confidence based on active responses between compounds. The approach demonstrates how leveraging large biological data through clustering can provide insight into toxicity mechanisms and develop predictive models.
The document summarizes a 2-day conference on qPCR and digital PCR taking place on July 11-12, 2016 in Philadelphia. Over 150 industry and academic experts will discuss the latest developments and applications of qPCR and dPCR across various fields such as healthcare, plant science, food science and environmental testing. The conference will feature keynote speakers, case study presentations, a poster session and interactive panels on topics including digital PCR applications, qPCR strategies, healthcare case studies, and plant/food/environmental case studies. Confirmed speakers include experts from academic institutions and companies.
Presentation at the Canadian Cancer Research Conference satellite bioinformatics.ca workshop. This one is an introduction to tcga, icgc and cosmic databases.
Introduction - OECD Seminar on Bioinformatics and Regulation of Microbial Pes...OECD Environment
24 June 2019: This OECD seminar presented and discussed the potential use of genome sequence, bioinformatic tools and databases in a regulatory decision process for microbial pesticides.
Cancer genome databases & Ecological databases Waliullah Wali
Introduction
Biological databases are libraries of life sciences information, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis.
Information contained in biological databases includes gene function, structure, localization, clinical effects of mutations as well as similarities of biological sequences and structures.
Cancer genome databases
COSMIC cancer database
COSMIC cancer database
COSMIC is an online database of somatically acquired mutations found in human cancer.
The database is freely available.
COSMIC cancer database
Types of data
Expert curation data
Genome-wide screen data
COSMIC cancer database
Expert curation data
Manually input by COSMIC expert curators.
Consists of comprehensive literature curation followed by subsequent updates.
Includes additional data points relevant to each disease and publication.
Provides accurate frequency data as mutation negative samples are specified.
COSMIC cancer database
Genome-wide screen data
Uploaded from publications reporting large scale genome screening data or imported from other databases such as TCGA and ICGC.
Provides unbiased molecular profiling of diseases while covering the whole genome.
Provides objective frequency data by interpreting non mutant genes across each genome.
Facilitates finding novel driver genes in cancer.
Enter into -
COSMIC cancer database
by typing http://cancer.sanger.ac.uk/cosmic
in the address bar of Browser
Searching Process
Examples
Examples
Examples
Examples
Ecological databases
Ecological databases
Ecological databases is a source for finding ecological datasets and quickly figuring out the best ways to use them.
BioOne
DataONE
GEOBASE
BioOne
BioOne is a nonprofit publisher that aims to make scientific research more accessible.
BioOne was established in 1999 in Washington, DC.
BioOne is Complete and open-access.
It serves a community of over 140 society and institutional publishers, 4,000 accessing institutions, and millions of researchers worldwide.
Enter into -
BioOne Ecological database
by typing http://www.bioone.org/
in the address bar of Browser
How bioinformatic and sequencing data might inform the regulatory process - O...OECD Environment
24 June 2019: This OECD seminar presented and discussed the potential use of genome sequence, bioinformatic tools and databases in a regulatory decision process for microbial pesticides.
How can Whole Genome Sequencing information be used to address data requireme...OECD Environment
This document discusses the potential use of whole genome sequencing data to address regulatory requirements for approval of microorganisms as active ingredients in plant protection products in the EU. It analyzes how genome sequencing could be used for species assignment, relationship to pathogens, distinction between Bacillus strains, production of metabolites, antibiotic resistance, genetic stability, risk assessment, and unequivocal identification of strains. While noting some potential benefits, it also describes limitations and problems with relying solely on genome sequencing data. It concludes that genome sequencing can be useful to exclude some issues but should not be a standard requirement, and that only reports on analyses—not the genome sequences themselves—should be included in dossiers.
CIIPro is an online cheminformatics portal for large-scale chemical data analysis. It contains two main components: CIIProfiler, which creates an optimized biological profile for compounds based on their activities in assays, and CIIP Nearest Neighbor (BioNN), which uses the biological profile to calculate biological similarity and identify biological nearest neighbors to predict activity. CIIPro aims to integrate in vitro high-throughput screening data with in vivo toxicity information to help identify potential toxicants and develop robust toxicity models.
CIIProCluster: Developing Read-Across Predictive Toxicity Models Using Big DataDaniel Russo
This document summarizes the CIIProCluster approach for developing predictive toxicity models using large biological and chemical data. It clusters bioassays based on the chemical substructures that activate them to identify mechanisms of toxicity. For oral acute toxicity data, it extracts biological assay profiles for compounds and clusters 1,948 assays based on relevant fingerprints. Evaluation of a cluster of cytotoxicity assays shows their potential for predicting oral toxicity when restricting predictions to those with high confidence based on active responses between compounds. The approach demonstrates how leveraging large biological data through clustering can provide insight into toxicity mechanisms and develop predictive models.
Invited talk presented at the Educational Session on "the use and abuse of chemical probes" chaired by Prof. Paul Workman about the Probe Miner resource and its use to help scientists assess and select chemical probes using publicly available data.
Biocuration activities for the International Cancer Genome Consortium (ICGC).Neuro, McGill University
The document discusses biocuration activities for the International Cancer Genome Consortium (ICGC). It provides information on the goals of ICGC including comprehensively analyzing 50 different cancer types/subtypes and making the genomic and clinical data publicly available. It describes the types of data being collected, standards being developed for data access and sharing, and current status of datasets released.
Presented at the Bioinformatics Seminar at the University of Arkansas, Little Rock on November 5, 2021.
PubChem (https://pubchem.ncbi.nlm.nih.gov) is a popular chemical database at the National Library of Medicine, National Institutes of Health. Arguably, PubChem is one of the largest chemical information resources in the public domain, with 111 million unique chemical structures, 1.39 million biological assays, and 292 million biological activity result outcomes. It also contains significant amounts of scientific research data and the inter-relationships between chemicals, proteins, genes, scientific literature, patents, and more. PubChem is a key resource for big data in chemistry and has been used in many studies for developing bioactivity and toxicity prediction models, discovering polypharmacologic (multi-target) ligands, and identifying new macromolecule targets of compounds (for drug-repurposing or off-target side effect prediction). It has also been used for cheminformatics education as well as chemical health and safety training. This presentation provides a high-level overview of PubChem’s data, tools, and services.
Presentation to the Department of Biology at the University of Windsor, Windsor, Ontario. The description and update of activities related to the International Cancer Genome Consortium (ICGC)
Effects of dots in HIV infected patients suffering from TuberculosisSubendu Mukherjee
The presentation summarizes a proposed clinical trial comparing two DOTS regimens for treating tuberculosis in HIV-positive and non-HIV patients. A project team was formed with defined roles. The objectives are to select trial sites, develop necessary documents, and prepare a budget. The trial aims to compare efficacy, safety, and quality of life outcomes between the regimens over 3 years. Standard operating procedures, a risk management plan, and project schedule were developed to manage the trial.
Development of FDA MicroDB: A Regulatory-Grade Microbial Reference DatabaseNathan Olson
"Development of FDA MicroDB: A Regulatory-Grade
Microbial Reference Database" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by the National Institute for Standards and Technology October 2014 by Heike Sichtig, PhD from the FDA and Luke Tallon from IGS UMSOM.
Microbiome Identification to Characterization: Pathogen Detection Webinar Ser...QIAGEN
This document discusses the development of rapid detection methods for microbial and microbiome analysis and their applications to human health. It provides an overview of QIAGEN's microbial qPCR products and discusses focused metagenomics applications like screening for antibiotic resistance genes in the food supply and human gut. Limitations of current methods are outlined and the benefits of qPCR for rapid, specific, and sensitive microbial detection are described.
Development of FDA MicroDB: A Regulatory-Grade Microbial Reference Databasenist-spin
"Development of FDA MicroDB: A Regulatory-Grade
Microbial Reference Database" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by National Institute for Standards and Technology October 2014 by Heike Sichtig, PhD from the FDA and Luke Tallon from IGS UMSOM.
PubChem as a resource for chemical information trainingSunghwan Kim
Presented at the 257th American Chemical Society (ACS) National Meeting in Orlando, FL (March 31, 2019). [CINF 13]
==== Abstract ====
Libraries at many large academic institutions provide chemical information training programs for students. However, these programs are based on commercial chemical information resources, which come with non-trivial subscription fees. These fees are often too expensive for small organizations, including many primarily undergraduate institutions (PUIs) and community colleges (CCs). It leads to disparity in access to chemical information as well as learning opportunities among students. This issue may be addressed at least in part by developing free online training programs based on public chemical databases, such as PubChem (https://pubchem.ncbi.nlm.nih.gov). PubChem has a great potential as an online resource for chemical education, but it also has important issues that students and teachers should keep in mind, such as data accuracy, data provenance, structure standardization, terminologies and so on. In this presentation, we will discuss various aspects of PubChem as a resource for chemical information training.
Microbiome Isolation and DNA Enrichment Protocol: Pathogen Detection Webinar ...QIAGEN
This slidedeck presents an easy-to-use workflow that allows selective isolation of microbial DNA from samples that are intrinsically rich in host DNA. This protocol includes steps for efficient depletion of host DNA while providing optimized conditions specific for bacterial lysis. This workflow is also specific for the identification of live bacteria, avoiding false results due to nucleic acids from dead bacteria. Enriched microbial DNA can be directly used in other molecular methods such as whole genome sequencing, qPCR and microarray assays.
The internet has provided access to unprecedented quantities of data. In the domain of chemistry specifically over the past decade the web has become populated with tens of millions of chemical structures and related properties, both experimental and predicted, together with tens of thousands of spectra and syntheses. The data have, to a large extent, remained disparate and disconnected. In recent years with the wave of Web 2.0 participation any chemist can contribute to both the sharing and validation of chemistry-related data whether it be via Wikipedia, the online encyclopedia, or one of the multiple public compound databases. Toxicologists commonly wish to source data, either for reference purposes, to support the development of models or, when experimental data are not available, predicted data will suffice. This presentation will offer a perspective of the type and quality of chemistry data available today, our experiences of building the ChemSpider public compound database to link together chemistry on the internet and our efforts to both encourage and enable even greater integration and connectivity for chemistry data for the community.
PubChem: A Public Chemical Information Resource for Big Data ChemistrySunghwan Kim
A web-seminar jointly organized by KWSE (Korean Woman Scientists & Engineers) and KWiSE (Korean-American Women in Science and Engineering). Presented on July 27, 2021.
Newer Diagnostic Modality in Tuberculosis.pptxBIMALESHYADAV2
The document discusses various conventional and recent advanced methods for tuberculosis diagnosis. Conventional methods discussed include microscopy using Ziehl-Neelsen staining and auramine rhodamine staining, culture on media like Lowenstein-Jensen and Middlebrook, and measurement of ADA levels. Recent advanced methods discussed include LED fluorescence microscopy, IGRA for infection detection, radiometric BACTEC system and MGIT system for faster culture, FASTPlaque TB test, Xpert MTB/RIF and Ultra assays using PCR, Truenat assays, automated NAATs, and line probe assays for molecular diagnosis and detection of drug resistance.
This presentation gives an overview of : Validation of microbiological methods , Considering some of the limitations and
Key criteria that may be applicable for assessment.
PubChem: a public chemical information resource for big data chemistrySunghwan Kim
PubChem is a public resource containing over 100 million unique chemical structures and 268 million bioactivity outcomes from assays. It aggregates data from over 750 sources and contains extensive information on chemical properties, biological activities, and related literature and patents. Users can search and access this data interactively through web interfaces or programmatically. As an example, bioactivity data from PubChem was used to develop predictive models for small molecule interactions with the retinoid X receptor alpha protein, achieving AUC scores over 0.7.
Dr David Galvin - IPPOSI Patient Reported Outcome Measured conference Oct 2018ipposi
The document summarizes the IPCOR study, which is collecting clinical and patient-reported data on prostate cancer patients in Ireland. The study is led by a team of investigators and aims to improve prostate cancer care in Ireland by establishing national standards, comparing outcomes to other countries, and conducting research. Data is collected longitudinally from patients and held securely to analyze outcomes, quality of life, and make recommendations to improve care while maintaining patient anonymity.
Erica Canzler - Advances and Lessons Learned in DecontaminationMatthew Kirkby
Advances in decontamination technologies and strategies were tested to help improve response to biological incidents. The Biological Operational Test and Evaluation Project tested three decontamination methods - vaporized hydrogen peroxide, bleach, and chlorine dioxide fumigation. Chlorine dioxide was most effective at reducing spore levels, while bleach produced the most waste. Overall costs were dominated by waste management. The methyl bromide fumigation study demonstrated the feasibility of using this technology for decontamination of structures. Efforts are also underway to develop strategies to safely restore contaminated underground transportation systems like subways following an incident.
1) The document describes an in-silico drug discovery project to identify inhibitors of the influenza virus polymerase PB1-PB2 protein complex.
2) The researchers used computational modeling techniques like benzene mapping, pharmacophore modeling, and molecular docking to identify potential binding sites on the PB1-PB2 complex and screen databases of drug-like molecules to discover top hit compounds.
3) Their methodology identified 50 top hit compounds from an initial screening that were further analyzed in secondary screening, and the 4 compounds with highest binding energies were identified as potential leads for inhibiting the PB1-PB2 interaction and warrant further testing in viral replication assays.
Biocuration 2013 - Fiona Brinkman - From genes, to genomes to networks, with ...fionabrinkman
The document discusses community-aided biocuration efforts led by Fiona Brinkman, beginning with the Pseudomonas Genome Project in 1997. It involved over 60 researchers from around the world collaboratively annotating the Pseudomonas aeruginosa genome via an online platform, producing over 1700 annotations. This early effort established the concept of "crowdsourcing" genome annotation. The current Pseudomonas Community Annotation Project (PseudoCAP) continues this work, maintaining continually updated annotations of the P. aeruginosa genome with contributions from over 150 researchers totaling over 2300 curated gene annotations.
This presentation provides an overview of the regulation of biotherapeutic medicines in Brazil. It discusses the development of regulations from 1976 to the current 2010 regulation, which takes specific approaches for biosimilars. The presentation outlines the pathways for approval, including an individual development pathway requiring full clinical data and a comparability pathway allowing reduced data if comparability to an existing product is shown. It provides details on non-clinical and clinical report requirements and considerations for both pathways. Finally, it discusses guidelines, partnerships and future perspectives on biological product regulation in Brazil.
Invited talk presented at the Educational Session on "the use and abuse of chemical probes" chaired by Prof. Paul Workman about the Probe Miner resource and its use to help scientists assess and select chemical probes using publicly available data.
Biocuration activities for the International Cancer Genome Consortium (ICGC).Neuro, McGill University
The document discusses biocuration activities for the International Cancer Genome Consortium (ICGC). It provides information on the goals of ICGC including comprehensively analyzing 50 different cancer types/subtypes and making the genomic and clinical data publicly available. It describes the types of data being collected, standards being developed for data access and sharing, and current status of datasets released.
Presented at the Bioinformatics Seminar at the University of Arkansas, Little Rock on November 5, 2021.
PubChem (https://pubchem.ncbi.nlm.nih.gov) is a popular chemical database at the National Library of Medicine, National Institutes of Health. Arguably, PubChem is one of the largest chemical information resources in the public domain, with 111 million unique chemical structures, 1.39 million biological assays, and 292 million biological activity result outcomes. It also contains significant amounts of scientific research data and the inter-relationships between chemicals, proteins, genes, scientific literature, patents, and more. PubChem is a key resource for big data in chemistry and has been used in many studies for developing bioactivity and toxicity prediction models, discovering polypharmacologic (multi-target) ligands, and identifying new macromolecule targets of compounds (for drug-repurposing or off-target side effect prediction). It has also been used for cheminformatics education as well as chemical health and safety training. This presentation provides a high-level overview of PubChem’s data, tools, and services.
Presentation to the Department of Biology at the University of Windsor, Windsor, Ontario. The description and update of activities related to the International Cancer Genome Consortium (ICGC)
Effects of dots in HIV infected patients suffering from TuberculosisSubendu Mukherjee
The presentation summarizes a proposed clinical trial comparing two DOTS regimens for treating tuberculosis in HIV-positive and non-HIV patients. A project team was formed with defined roles. The objectives are to select trial sites, develop necessary documents, and prepare a budget. The trial aims to compare efficacy, safety, and quality of life outcomes between the regimens over 3 years. Standard operating procedures, a risk management plan, and project schedule were developed to manage the trial.
Development of FDA MicroDB: A Regulatory-Grade Microbial Reference DatabaseNathan Olson
"Development of FDA MicroDB: A Regulatory-Grade
Microbial Reference Database" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by the National Institute for Standards and Technology October 2014 by Heike Sichtig, PhD from the FDA and Luke Tallon from IGS UMSOM.
Microbiome Identification to Characterization: Pathogen Detection Webinar Ser...QIAGEN
This document discusses the development of rapid detection methods for microbial and microbiome analysis and their applications to human health. It provides an overview of QIAGEN's microbial qPCR products and discusses focused metagenomics applications like screening for antibiotic resistance genes in the food supply and human gut. Limitations of current methods are outlined and the benefits of qPCR for rapid, specific, and sensitive microbial detection are described.
Development of FDA MicroDB: A Regulatory-Grade Microbial Reference Databasenist-spin
"Development of FDA MicroDB: A Regulatory-Grade
Microbial Reference Database" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by National Institute for Standards and Technology October 2014 by Heike Sichtig, PhD from the FDA and Luke Tallon from IGS UMSOM.
PubChem as a resource for chemical information trainingSunghwan Kim
Presented at the 257th American Chemical Society (ACS) National Meeting in Orlando, FL (March 31, 2019). [CINF 13]
==== Abstract ====
Libraries at many large academic institutions provide chemical information training programs for students. However, these programs are based on commercial chemical information resources, which come with non-trivial subscription fees. These fees are often too expensive for small organizations, including many primarily undergraduate institutions (PUIs) and community colleges (CCs). It leads to disparity in access to chemical information as well as learning opportunities among students. This issue may be addressed at least in part by developing free online training programs based on public chemical databases, such as PubChem (https://pubchem.ncbi.nlm.nih.gov). PubChem has a great potential as an online resource for chemical education, but it also has important issues that students and teachers should keep in mind, such as data accuracy, data provenance, structure standardization, terminologies and so on. In this presentation, we will discuss various aspects of PubChem as a resource for chemical information training.
Microbiome Isolation and DNA Enrichment Protocol: Pathogen Detection Webinar ...QIAGEN
This slidedeck presents an easy-to-use workflow that allows selective isolation of microbial DNA from samples that are intrinsically rich in host DNA. This protocol includes steps for efficient depletion of host DNA while providing optimized conditions specific for bacterial lysis. This workflow is also specific for the identification of live bacteria, avoiding false results due to nucleic acids from dead bacteria. Enriched microbial DNA can be directly used in other molecular methods such as whole genome sequencing, qPCR and microarray assays.
The internet has provided access to unprecedented quantities of data. In the domain of chemistry specifically over the past decade the web has become populated with tens of millions of chemical structures and related properties, both experimental and predicted, together with tens of thousands of spectra and syntheses. The data have, to a large extent, remained disparate and disconnected. In recent years with the wave of Web 2.0 participation any chemist can contribute to both the sharing and validation of chemistry-related data whether it be via Wikipedia, the online encyclopedia, or one of the multiple public compound databases. Toxicologists commonly wish to source data, either for reference purposes, to support the development of models or, when experimental data are not available, predicted data will suffice. This presentation will offer a perspective of the type and quality of chemistry data available today, our experiences of building the ChemSpider public compound database to link together chemistry on the internet and our efforts to both encourage and enable even greater integration and connectivity for chemistry data for the community.
PubChem: A Public Chemical Information Resource for Big Data ChemistrySunghwan Kim
A web-seminar jointly organized by KWSE (Korean Woman Scientists & Engineers) and KWiSE (Korean-American Women in Science and Engineering). Presented on July 27, 2021.
Newer Diagnostic Modality in Tuberculosis.pptxBIMALESHYADAV2
The document discusses various conventional and recent advanced methods for tuberculosis diagnosis. Conventional methods discussed include microscopy using Ziehl-Neelsen staining and auramine rhodamine staining, culture on media like Lowenstein-Jensen and Middlebrook, and measurement of ADA levels. Recent advanced methods discussed include LED fluorescence microscopy, IGRA for infection detection, radiometric BACTEC system and MGIT system for faster culture, FASTPlaque TB test, Xpert MTB/RIF and Ultra assays using PCR, Truenat assays, automated NAATs, and line probe assays for molecular diagnosis and detection of drug resistance.
This presentation gives an overview of : Validation of microbiological methods , Considering some of the limitations and
Key criteria that may be applicable for assessment.
PubChem: a public chemical information resource for big data chemistrySunghwan Kim
PubChem is a public resource containing over 100 million unique chemical structures and 268 million bioactivity outcomes from assays. It aggregates data from over 750 sources and contains extensive information on chemical properties, biological activities, and related literature and patents. Users can search and access this data interactively through web interfaces or programmatically. As an example, bioactivity data from PubChem was used to develop predictive models for small molecule interactions with the retinoid X receptor alpha protein, achieving AUC scores over 0.7.
Dr David Galvin - IPPOSI Patient Reported Outcome Measured conference Oct 2018ipposi
The document summarizes the IPCOR study, which is collecting clinical and patient-reported data on prostate cancer patients in Ireland. The study is led by a team of investigators and aims to improve prostate cancer care in Ireland by establishing national standards, comparing outcomes to other countries, and conducting research. Data is collected longitudinally from patients and held securely to analyze outcomes, quality of life, and make recommendations to improve care while maintaining patient anonymity.
Erica Canzler - Advances and Lessons Learned in DecontaminationMatthew Kirkby
Advances in decontamination technologies and strategies were tested to help improve response to biological incidents. The Biological Operational Test and Evaluation Project tested three decontamination methods - vaporized hydrogen peroxide, bleach, and chlorine dioxide fumigation. Chlorine dioxide was most effective at reducing spore levels, while bleach produced the most waste. Overall costs were dominated by waste management. The methyl bromide fumigation study demonstrated the feasibility of using this technology for decontamination of structures. Efforts are also underway to develop strategies to safely restore contaminated underground transportation systems like subways following an incident.
1) The document describes an in-silico drug discovery project to identify inhibitors of the influenza virus polymerase PB1-PB2 protein complex.
2) The researchers used computational modeling techniques like benzene mapping, pharmacophore modeling, and molecular docking to identify potential binding sites on the PB1-PB2 complex and screen databases of drug-like molecules to discover top hit compounds.
3) Their methodology identified 50 top hit compounds from an initial screening that were further analyzed in secondary screening, and the 4 compounds with highest binding energies were identified as potential leads for inhibiting the PB1-PB2 interaction and warrant further testing in viral replication assays.
Biocuration 2013 - Fiona Brinkman - From genes, to genomes to networks, with ...fionabrinkman
The document discusses community-aided biocuration efforts led by Fiona Brinkman, beginning with the Pseudomonas Genome Project in 1997. It involved over 60 researchers from around the world collaboratively annotating the Pseudomonas aeruginosa genome via an online platform, producing over 1700 annotations. This early effort established the concept of "crowdsourcing" genome annotation. The current Pseudomonas Community Annotation Project (PseudoCAP) continues this work, maintaining continually updated annotations of the P. aeruginosa genome with contributions from over 150 researchers totaling over 2300 curated gene annotations.
This presentation provides an overview of the regulation of biotherapeutic medicines in Brazil. It discusses the development of regulations from 1976 to the current 2010 regulation, which takes specific approaches for biosimilars. The presentation outlines the pathways for approval, including an individual development pathway requiring full clinical data and a comparability pathway allowing reduced data if comparability to an existing product is shown. It provides details on non-clinical and clinical report requirements and considerations for both pathways. Finally, it discusses guidelines, partnerships and future perspectives on biological product regulation in Brazil.
1. CIIPro: An online
cheminformatics portal for large
scale chemical data analysis
Daniel P Russo,1 Wenyi Wang,1 Daniel Pinolini,1 Marlene T Kim,1,2 and
Hao Zhu1, 2
Zhu Research Group
1The Rutgers Center for Computational and Integrative Biology, Camden, New Jersey 08102;
2Department of Chemistry, Rutgers University, Camden, New Jersey 08102;
2. Outline
• Motivation: Current state of toxicology
• High throughput screening
• In vitro-in vivo correlation
• CIIPro: An online cheminformatics portal
• CIIProfiler: Chemical in vitro-in vivo profiling
• CIIP Nearest Neighbor: Using CIIPro to find biological
nearest neighbors
• Demonstration
• The future of CIIPro
• Motivation: Current state of toxicology
• High throughput screening
• In vitro-in vivo correlation
• CIIPro: An online cheminformatics portal
• CIIProfiler: Chemical in vitro-in vivo profiling
• CIIP Nearest Neighbor: Using CIIPro to find biological
nearest neighbors
• Demonstration
• The future of CIIPro
2
3. Current State of Toxicology: Traditional toxicology testing
CIIPro: Current State of Toxicology 3
$20M
Cancer
ReproTox
DevTox
NeuroTox
PulmonaryTox
ImmunoTox
Chemical
Slide courtesy of Dr. Richard Judson, U.S. EPA
4. Current State of Toxicology: High throughput screening
CIIPro: Current State of Toxicology 4Collins, F. S., Gray, G. M. & Bucher, J. R. Transforming Environmental Health
Protection. Science 319, 906–907 (2008).
5. Current State of Toxicology: What can we learn?
CIIPro: Current State of Toxicology 5
Zhu, H. et al. Big data in chemical toxicity research: the use of high-throughput screening
assays to identify potential toxicants. Chem. Res. Toxicol. 27, 1643–1651 (2014).
6. Current State of Toxicology: From databases to researchers
CIIPro: Current State of Toxicology 6
Growing pool
of in vitro
data
Chem. Res. Tox. 2014; (27) 1643-1651
7. CIIPro: An online cheminformatics portal
CIIPro: An online Cheminformatics portal 7
8. Outline
• Motivation: Current state of toxicology
• High throughput screening
• In vitro-in vivo correlation
• CIIPro: An online cheminformatics portal
• CIIProfiler: Chemical in vitro-in vivo profiling
• CIIP Nearest Neighbor: Using CIIPro to find biological
nearest neighbors
• Demonstration
• The future of CIIPro
8
9. Target
Compounds
I. Create Optimized
Biological
Profile
II a. Calculate
Biological Similarity
II b. Calculate
Biological Nearest
Neighbors
II c. Evaluate
Biological Activity
Using Biological
Nearest Neighbors
I. CIIProfiler
II. CIIP BioNN
The four steps of CIIPro
10. Outline
• Motivation: Current state of toxicology
• High throughput screening
• In vitro-in vivo correlation
• CIIPro: An online cheminformatics portal
• CIIProfiler: Chemical in vitro-in vivo profiling
• CIIP Nearest Neighbor: Using CIIPro to find biological nearest
neighbors
• Demonstration
• The future of CIIPro
10
I. Create a biological profile
12. Outline
• Motivation: Current state of toxicology
• High throughput screening
• In vitro in vivo correlation
• CIIPro: An online cheminformatics portal
• CIIProfiler: Chemical in vitro, in vivo profiling
• CIIP Nearest Neighbor: Using CIIPro to find biological
nearest neighbors
• Demonstration
• The future of CIIPro
12
II a. Use biological profile to
calculate biological similarity
II b. Use biological similarity create
biological nearest neighbors
II c. Use biological nearest
neighbors to evaluate biological
activity
14. Outline
• Motivation: Current state of toxicology
• High throughput screening
• In vitro in vivo correlation
• CIIPro: An online cheminformatics portal
• CIIProfiler: Chemical in vitro, in vivo profiling
• CIIP Predictor: Using CIIPro to create robust toxicity models
• Demonstration
• The future of CIIPro
14
15. Demonstration
Demonstration 15
*Wang W., Kim M. T., Sedykh A., and Zhu, H. Developing Enhanced Blood–Brain Barrier Permeability
Models: Integrating External Bio-Assay Data in QSAR Modeling. Pharm Res 32, 3055–3065 (2015).
Blood Brain Barrier
Dataset* Overview
114
Barrier
Permeable
Compounds
1
114
Barrier
Impermeable
Compounds
0
16. Outline
• Motivation: Current state of toxicology
• High throughput screening
• In vitro in vivo correlation
• CIIPro: An online cheminformatics portal
• CIIProfiler: Chemical in vitro, in vivo profiling
• CIIP Predictor: Using CIIPro to create robust toxicity models
• Demonstration
• The future of CIIPro
16
17. The future of CIIPro 17
Potential
Toxicants
Optimized
Biological Profile
Chemical
Descriptors
In House Animal
Toxicity Data
Toxic
Non-toxic
The future of CIIPro
18. Current State of Toxicology: From databases to researchers
CIIPro: Current State of Toxicology 18
Growing pool
of in vitro
data
Chem. Res. Tox. 2014; (27) 1643-1651
19. Acknowledgements 19
Funding resources:
• National Institute of Health:
1R15ES023148
• Society of Toxicology: Colgate-
Palmolive Grant for Alternative
Research
Acknowledgments Acknowledgments:
Zhu Research Group
Special Thanks to:
Hao Zhu
Marlene Kim
Wenyi Wang
Daniel Pinolini
Kevin Abbey
Zhu Research Group
20. CIIPro: An online cheminformatics portal
CIIPro: An online Cheminformatics portal 20
Questions?
22. Current State of Toxicology: High throughput screening
CIIPro: Current State of Toxicology 22
ToxCast
Growing pool
of in vitro
data
CTD
Tox21
Animal
toxicity data
In vitro - in vivo
correlation
23. Current State of Toxicology: What can we learn from the in vitro data?
CIIPro: Current State of Toxicology 23
Growing pool
of in vitro
data
Animal
toxicity data
Animal
toxicity data
Animal
toxicity data
Animal
toxicity data
Editor's Notes
Large amounts of chemicals without toxicity information
High rate of failure of drugs due to toxicity, adverse drug reactions owing to a lack of understanding of toxicology mechanisms
Ethical concerns on the use of animals, high cost of testing, and difficultly in species extrapolation has pressured alternative methods to prioritize chemical toxicity assessment
-In vitro assays
QSAR, readacross, etc
Large amounts of chemicals without toxicity information
High rate of failure of drugs due to toxicity, adverse drug reactions owing to a lack of understanding of toxicology mechanisms
Ethical concerns on the use of animals, high cost of testing, and difficultly in species extrapolation has pressured alternative methods to prioritize chemical toxicity assessment
-In vitro assays
QSAR, readacross, etc
Large amounts of chemicals without toxicity information
High rate of failure of drugs due to toxicity, adverse drug reactions owing to a lack of understanding of toxicology mechanisms
Ethical concerns on the use of animals, high cost of testing, and difficultly in species extrapolation has pressured alternative methods to prioritize chemical toxicity assessment
-In vitro assays
QSAR, readacross, etc
HTS uses robotics in various in vitro cellular assays in a rapid standardized manner
Several fields such as drug discovery and toxicology have undertook large HTS efforts (PDSP, ToxCast) yielding a wealth of compounds linked to rich, biological data
Updated daily, various public repositories (i.e, PubChem) have curated, stored, and made these data publicly available.
Compound response data from PubChem can offer unique insights to a compounds’ in vivo response
HTS uses robotics in various in vitro cellular assays in a rapid standardized manner
Several fields such as drug discovery and toxicology have undertook large HTS efforts (PDSP, ToxCast) yielding a wealth of compounds linked to rich, biological data
Updated daily, various public repositories (i.e, PubChem) have curated, stored, and made these data publicly available.
Compound response data from PubChem can offer unique insights to a compounds’ in vivo response
HTS uses robotics in various in vitro cellular assays in a rapid standardized manner
Several fields such as drug discovery and toxicology have undertook large HTS efforts (PDSP, ToxCast) yielding a wealth of compounds linked to rich, biological data
Updated daily, various public repositories (i.e, PubChem) have curated, stored, and made these data publicly available.
Compound response data from PubChem can offer unique insights to a compounds’ in vivo response
HTS uses robotics in various in vitro cellular assays in a rapid standardized manner
Several fields such as drug discovery and toxicology have undertook large HTS efforts (PDSP, ToxCast) yielding a wealth of compounds linked to rich, biological data
Updated daily, various public repositories (i.e, PubChem) have curated, stored, and made these data publicly available.
Compound response data from PubChem can offer unique insights to a compounds’ in vivo response
HTS uses robotics in various in vitro cellular assays in a rapid standardized manner
Several fields such as drug discovery and toxicology have undertook large HTS efforts (PDSP, ToxCast) yielding a wealth of compounds linked to rich, biological data
Updated daily, various public repositories (i.e, PubChem) have curated, stored, and made these data publicly available.
Compound response data from PubChem can offer unique insights to a compounds’ in vivo response
HTS uses robotics in various in vitro cellular assays in a rapid standardized manner
Several fields such as drug discovery and toxicology have undertook large HTS efforts (PDSP, ToxCast) yielding a wealth of compounds linked to rich, biological data
Updated daily, various public repositories (i.e, PubChem) have curated, stored, and made these data publicly available.
Compound response data from PubChem can offer unique insights to a compounds’ in vivo response
HTS uses robotics in various in vitro cellular assays in a rapid standardized manner
Several fields such as drug discovery and toxicology have undertook large HTS efforts (PDSP, ToxCast) yielding a wealth of compounds linked to rich, biological data
Updated daily, various public repositories (i.e, PubChem) have curated, stored, and made these data publicly available.
Compound response data from PubChem can offer unique insights to a compounds’ in vivo response
HTS uses robotics in various in vitro cellular assays in a rapid standardized manner
Several fields such as drug discovery and toxicology have undertook large HTS efforts (PDSP, ToxCast) yielding a wealth of compounds linked to rich, biological data
Updated daily, various public repositories (i.e, PubChem) have curated, stored, and made these data publicly available.
Compound response data from PubChem can offer unique insights to a compounds’ in vivo response
HTS uses robotics in various in vitro cellular assays in a rapid standardized manner
Several fields such as drug discovery and toxicology have undertook large HTS efforts (PDSP, ToxCast) yielding a wealth of compounds linked to rich, biological data
Updated daily, various public repositories (i.e, PubChem) have curated, stored, and made these data publicly available.
Compound response data from PubChem can offer unique insights to a compounds’ in vivo response