This is an opener to the various requirements as in hardware and softwares needed to run molecular docking computations, including the various steps invloved in running molecular docking.
In this presentation, delve into the capabilities of MOE and discover how it enables scientists to:
Accelerate Drug Discovery: Streamline the drug discovery process with MOE's advanced molecular modeling techniques, allowing for efficient virtual screening, lead optimization, and structure-activity relationship (SAR) analysis.
Predict Molecular Properties: Leverage MOE's predictive modeling capabilities to forecast various molecular properties, including ligand-receptor interactions, protein-ligand binding affinity, and ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties.
Visualize Complex Molecular Systems: Gain deeper insights into molecular structures and dynamics through MOE's intuitive visualization tools, facilitating the interpretation of simulation results and aiding in decision-making processes.
Collaborate Effectively: Foster collaboration among interdisciplinary research teams with MOE's robust data sharing and collaborative features, enabling seamless communication and knowledge exchange.
Stay at the Forefront of Research: Keep pace with the latest advancements in molecular modeling and computational chemistry through MOE's regular updates and integration of cutting-edge algorithms and methodologies.
Molecular docking is a method for predicting how two molecules, such as a ligand and its protein target, will interact and fit together in three dimensions. Docking has become an important tool in drug discovery for identifying potential binding conformations between drug candidates and protein targets. The key steps in a typical docking workflow involve selecting the receptor and ligand molecules, then using software to computationally predict the orientation of binding and evaluate the fit through scoring functions. Popular molecular docking software packages include AutoDock, GOLD, and Glide. Applications of docking include virtual screening in drug discovery and lead optimization.
This document discusses computational aided drug design. It begins by defining drug and the drug design process. It describes that the selected drug molecule should be an organic small molecule that is complementary in shape and oppositely charged to the target biomolecule. It then discusses ligand based and structure based drug design approaches. Various techniques used in drug design are also summarized such as x-ray crystallography, NMR, homology modeling, and computer aided drug design. Benefits of computational aided drug design include streamlining drug discovery, eliminating compounds with undesirable properties, and identifying and optimizing new drugs in a time and cost effective manner.
The document describes a distributed approach for running the C-Ranker peptide identification algorithm across multiple machines. C-Ranker currently runs on a single machine, but processing large datasets can take a long time. The proposed solution divides the dataset across multiple machines running C-Ranker in parallel. The results show the distributed approach reduces execution time compared to running C-Ranker on a single machine or using an Apache Hadoop cluster. For example, processing a 48KB dataset took 9.2 hours distributed versus 15.2 hours on a single machine. The distributed approach also better manages resources and has lower costs than maintaining an Hadoop cluster.
USUGM 2014 - Xin Zhang (Cubist): A chemistry friendly system integrating drug...ChemAxon
This document discusses Cubist Pharmaceuticals' DT workbench, a web-based platform for integrating drug design tools. It introduces drug metabolism and how computational models can help predict sites of metabolism to improve drug candidates. The workbench standardizes inputs using templates and utilizes Marvin components for drawing, viewing, and analyzing structures. A case study demonstrates using the workbench to identify the metabolic liability of Ticrynafen, perform lead hopping to find alternatives, and evaluate new structures. The workbench reduces learning curves and allows customizing Marvin tools for various needs like highlighting predicted sites of metabolism.
This document discusses Cubist Pharmaceuticals' DT workbench, a web-based platform for integrating drug design tools. It introduces drug metabolism and how metabolites can impact drug failures. The workbench was created to make prediction models more user-friendly and accessible to chemists. A case study demonstrates using the workbench to predict the metabolism site of ticrynafen, conduct lead hopping to replace problematic groups, and evaluate new structures. The workbench utilizes Marvin components like the sketch applet for drawing and customized viewers for results. This allows flexible, adaptable interfaces without end user installation.
How we Built a Large Scale Matched Pair Analysis Engine (MCPairs) using OpenE...Al Dossetter
MCPairs performed Matched Molecular Pair Analysis on large scale to build databases of exploitable knowledge which is accessible for Drug Discovery to accelerate research projects. The talk describes how we did this and some of the challenges.
IRJET - Machine Learning for Diagnosis of DiabetesIRJET Journal
This document describes a study that uses machine learning models to predict whether a person has diabetes based on patient data. The researchers created several classification models using algorithms like logistic regression and support vector machines on a diabetes dataset. The models with the highest accuracy at predicting diabetes were random forest and gradient boosting. An Android app was also developed to input patient data, run the predictions from the trained models, and display the results to help diagnose diabetes. The goal is to help reduce diabetes rates and healthcare costs by improving diagnosis.
In this presentation, delve into the capabilities of MOE and discover how it enables scientists to:
Accelerate Drug Discovery: Streamline the drug discovery process with MOE's advanced molecular modeling techniques, allowing for efficient virtual screening, lead optimization, and structure-activity relationship (SAR) analysis.
Predict Molecular Properties: Leverage MOE's predictive modeling capabilities to forecast various molecular properties, including ligand-receptor interactions, protein-ligand binding affinity, and ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties.
Visualize Complex Molecular Systems: Gain deeper insights into molecular structures and dynamics through MOE's intuitive visualization tools, facilitating the interpretation of simulation results and aiding in decision-making processes.
Collaborate Effectively: Foster collaboration among interdisciplinary research teams with MOE's robust data sharing and collaborative features, enabling seamless communication and knowledge exchange.
Stay at the Forefront of Research: Keep pace with the latest advancements in molecular modeling and computational chemistry through MOE's regular updates and integration of cutting-edge algorithms and methodologies.
Molecular docking is a method for predicting how two molecules, such as a ligand and its protein target, will interact and fit together in three dimensions. Docking has become an important tool in drug discovery for identifying potential binding conformations between drug candidates and protein targets. The key steps in a typical docking workflow involve selecting the receptor and ligand molecules, then using software to computationally predict the orientation of binding and evaluate the fit through scoring functions. Popular molecular docking software packages include AutoDock, GOLD, and Glide. Applications of docking include virtual screening in drug discovery and lead optimization.
This document discusses computational aided drug design. It begins by defining drug and the drug design process. It describes that the selected drug molecule should be an organic small molecule that is complementary in shape and oppositely charged to the target biomolecule. It then discusses ligand based and structure based drug design approaches. Various techniques used in drug design are also summarized such as x-ray crystallography, NMR, homology modeling, and computer aided drug design. Benefits of computational aided drug design include streamlining drug discovery, eliminating compounds with undesirable properties, and identifying and optimizing new drugs in a time and cost effective manner.
The document describes a distributed approach for running the C-Ranker peptide identification algorithm across multiple machines. C-Ranker currently runs on a single machine, but processing large datasets can take a long time. The proposed solution divides the dataset across multiple machines running C-Ranker in parallel. The results show the distributed approach reduces execution time compared to running C-Ranker on a single machine or using an Apache Hadoop cluster. For example, processing a 48KB dataset took 9.2 hours distributed versus 15.2 hours on a single machine. The distributed approach also better manages resources and has lower costs than maintaining an Hadoop cluster.
USUGM 2014 - Xin Zhang (Cubist): A chemistry friendly system integrating drug...ChemAxon
This document discusses Cubist Pharmaceuticals' DT workbench, a web-based platform for integrating drug design tools. It introduces drug metabolism and how computational models can help predict sites of metabolism to improve drug candidates. The workbench standardizes inputs using templates and utilizes Marvin components for drawing, viewing, and analyzing structures. A case study demonstrates using the workbench to identify the metabolic liability of Ticrynafen, perform lead hopping to find alternatives, and evaluate new structures. The workbench reduces learning curves and allows customizing Marvin tools for various needs like highlighting predicted sites of metabolism.
This document discusses Cubist Pharmaceuticals' DT workbench, a web-based platform for integrating drug design tools. It introduces drug metabolism and how metabolites can impact drug failures. The workbench was created to make prediction models more user-friendly and accessible to chemists. A case study demonstrates using the workbench to predict the metabolism site of ticrynafen, conduct lead hopping to replace problematic groups, and evaluate new structures. The workbench utilizes Marvin components like the sketch applet for drawing and customized viewers for results. This allows flexible, adaptable interfaces without end user installation.
How we Built a Large Scale Matched Pair Analysis Engine (MCPairs) using OpenE...Al Dossetter
MCPairs performed Matched Molecular Pair Analysis on large scale to build databases of exploitable knowledge which is accessible for Drug Discovery to accelerate research projects. The talk describes how we did this and some of the challenges.
IRJET - Machine Learning for Diagnosis of DiabetesIRJET Journal
This document describes a study that uses machine learning models to predict whether a person has diabetes based on patient data. The researchers created several classification models using algorithms like logistic regression and support vector machines on a diabetes dataset. The models with the highest accuracy at predicting diabetes were random forest and gradient boosting. An Android app was also developed to input patient data, run the predictions from the trained models, and display the results to help diagnose diabetes. The goal is to help reduce diabetes rates and healthcare costs by improving diagnosis.
The Proteomics and Metabolomics Shared Resource (PMSR) at Georgetown University provides proteomics and metabolomics services and expertise. The document describes the PMSR's integrated proteomics workflow including 2D gel-based analysis, DIGE, spot picking, and MALDI TOF/TOF mass spectrometry for protein identification. Liquid chromatography-based proteomics using iTRAQ/ICAT labeling for quantitative analysis and a nano LC-QSTAR ELITE mass spectrometer are also described. The PMSR supports small molecule profiling and quantitation using UPLC-TOFMS and metabolomics applications.
Rashad Badrawi has training in biological and computer sciences. He has a BS in Biology, MS degrees in Pharmacology and Information Systems. He has worked as a software engineer and bioinformatics specialist at several universities and companies. Some of his projects include building GeneMania's data warehouse, translating the BIND interactions database, and designing interoperability between Virtual Cell and systems biology standards. His strengths include being a self-starter, team player, and mentor who enjoys building products from start to finish while keeping up with advances in biomedical informatics.
Amol Ashok Kunde is seeking a position in neurology development. He has a Master's in Computational biology and 1.5 years of research experience. His experience includes molecular biology techniques, using drug discovery software, and working as an assistant manager. He has experience designing automated pipelines for analysis, classifying brain tumors using neural networks, and insilico drug design.
Artificial Intelligence and Machine Learning Operated Pesticide SprayerIRJET Journal
The document describes the development of an artificially intelligent and machine learning operated pesticide sprayer. The sprayer uses computer vision to identify healthy and unhealthy plant leaves and only sprays pesticides on leaves that require treatment. This helps reduce overuse of pesticides, saves time and labor for farmers, and protects soil health. The sprayer is designed with a raspberry pi microcontroller that controls actuators like motors and pumps. Machine learning algorithms are trained on image datasets to recognize healthy and unhealthy leaves, and the sprayer is programmed to actuate pesticide spraying accordingly. The system aims to automate pesticide application in agriculture for improved accuracy, efficiency and reduced human effort.
Pharma Research Automation by Connecting Researchers with Robots and Systems ...camunda services GmbH
The discovery of new therapeutic molecule has become a highly demanding endeavour. The main goal is to find an effective molecule, i.e. one that address a particular disease. On this path many conditions need to be met. A critical one is to ensure the safety of the molecule, meaning that it only targets the disease and nothing more. Next, while having ensured safety and effectiveness, another question that arises is the suitability for production, i.e. is it even possible to produce the molecule consistently and at scale over the many years the medicine will be available on the market? This is especially challenging for biologics, i.e. large therapeutic molecules produced by living cells.
Looking at the software landscape in pharma research we are confronted with a highly heterogeneous view, involving a broad combinations of different software systems with various interfacing possibilities. Molecules are tracked in registration systems, lab information management systems or electronic lab notebooks store process data. Requests between labs are handled by requesting systems, robotic systems (liquid handlers, analytics) produce large data and we can’t ignore the amount of spreadsheets used to document or calculate.
While faced with complex questions, researchers have developed a series of individual methods that, on their own, answer or help with a small part of the questions above. The true value comes by automating the combination of these methods into end-to-end processes that answer the full research question. Thus it is more than fitting to use business process modelling not only to describe the research process, but to also execute it.
In this presentation we show the use of business process modelling to map and drive research processes stretching over researcher decision points, backend systems and robots. In particular, our current robot integration is to treat robots as external systems where the orchestration engine configures, monitors and collects results while the user is still fully in charge of loading and triggering an actual run. Unlike fully automated setups, a research environment demands flexibility as processes and their branches change. Even so, we show by using executable business processes in the pharma industry research, we increase throughput, transparency, standardization and time-to-results .
This document provides a summary of Md. Ariful Islam's background and qualifications. He is a PhD candidate in Computer Science at Stony Brook University focused on modeling, simulation, and formal verification of complex software and dynamical systems. He has extensive skills in various modeling, simulation, optimization, and programming languages and tools.
SooryaKiran Bioinformatics is a global bioinformatics solutions provider that focuses on customized bioinformatics services and products. It develops algorithms and software for biological sequence analysis, structure prediction, and other areas. Key products include tools for sequence generation, analysis, and homology identification. The company collaborates with research institutions and has provided solutions for SNP analysis, genome analysis, and mitochondrial DNA analysis to clients around the world.
This document discusses molecular modelling and docking techniques. It describes molecular docking as a computational method to predict how two molecules, such as a protein and ligand, interact and bind with each other. It outlines key stages in docking like receptor and ligand selection and preparation. It also discusses different docking tools, types of docking including rigid and flexible docking, scoring functions used to evaluate predicted complexes, and examples of specific enzymes like dihydrofolate reductase that can be modeled.
Emerging Challenges for Artificial Intelligence in Medicinal ChemistryEd Griffen
Presentation by Dr Ed Griffen of MedChemica Ltd, at The IBSA Conference "How Artificial Intelligence Can Change the Pharmaceutical Landscape“ - LUGANO, October 9th 2019.
- Suraj S Hanchate is seeking a position as an Oracle Database Administrator with over 5 years of experience in installing, configuring, and maintaining Oracle databases.
- He has extensive experience with Oracle 10g, 11g, and 12c databases and has worked on projects for electricity departments in Bangalore, Goa, and Jaipur.
- His responsibilities have included database backups, patching, performance tuning, and troubleshooting administration issues.
1) The document discusses integrating OpenClinica, an open-source clinical data management system, with a patient monitoring tool (PMT) to improve efficiency in clinical data management for studies conducted by DNDi and PHPT.
2) Key objectives of the integration are to reduce the time to obtain clean study data sets and decrease error rates by facilitating real-time monitoring of patient data entered into OpenClinica.
3) The methodology developed uses a community data mart to transfer study data from OpenClinica to the PMT database, allowing monitors to access collated subject data through a single interface and improving monitoring.
Protein structure-based design and engineering can provide insights into protein function and improve protein properties through molecular modelling and targeted mutations. Molecular modelling generates 3D protein structures from sequences to understand structure-function relationships and identify active sites, domains, and other structural features. It also enables large-scale in silico mutation screening to focus experimental efforts on the most promising recombinant protein variants for applications in health, environment, and technology.
DNA Query Language DNAQL: A Novel ApproachEditor IJCATR
This document describes a proposed DNA Query Language (DNAQL) that could allow researchers to query DNA databases in a more intuitive way compared to SQL. The DNAQL is presented as a novel approach that would introduce an abstraction layer between the user interface and database, translating queries in a familiar biochemical language into SQL understood by the database. This could help alleviate challenges biochemistry researchers face in accessing and analyzing protein data from databases. The document provides background on DNA computing and challenges in current databases, reviews related work on biological database querying, and describes the proposed methodology for DNA sequencing and DNAQL.
This document summarizes the services provided by an organization that conducts research and training in areas related to biotechnology and pharmaceuticals. They provide online and in-person training programs and research projects in topics such as bioinformatics, drug design, genomics, and proteomics. They have completed over 20 research projects in the past year that have led to international publications. They also organize workshops on drug discovery and genomics at universities and institutions around the world, both in-person and online. Their goal is to strengthen the skills and careers of young researchers through hands-on training and research experience.
A systematic review of network analyst - PubricaPubrica
In a Systematic Review Writing, the network analyst is a bioinformatics tool designed to perform efficient PPI network analysis for data generated from gene expression experiments the following contents explain about the network analyst and their methods, in brief, using the help of Pubrica blog.
Continue Reading: https://bit.ly/3nAa3ek
Reference: https://pubrica.com/services/research-services/systematic-review/
Why Pubrica?
When you order our services, Plagiarism free|on Time|outstanding customer support|Unlimited Revisions support|High-quality Subject Matter Experts.
Contact us :
Web: https://pubrica.com/
Blog: https://pubrica.com/academy/
Email: sales@pubrica.com
WhatsApp : +91 9884350006
United Kingdom: +44- 74248 10299
This document provides an overview of biotechnology and bioinformatics for students. It discusses the main branches of biotechnology including microbiology, biochemistry, cell biology, and bioinformatics. Bioinformatics is defined as involving bio data storage, sequence analysis, and computer aided drug design. Molecular docking is described as a process to determine the compatibility of two molecules like a lock and key through binding of ligands and proteins. The document outlines the steps in molecular docking, types of docking, and softwares used. Finally, it discusses several important biological databases used in bioinformatics research including NCBI, SwissADME, DrugBank, and PDB.
This document provides information about the Metabolic Engineering course taught by Dr. Lovely at Noida Institute of Engineering and Technology. It includes details about the course syllabus, units covered, evaluation scheme, course objectives and outcomes. The key topics covered are metabolic flux analysis, experimental determination of metabolic fluxes, computational modelling of biological networks, and industrial applications of metabolic engineering including pathway engineering strategies for production of commercially important metabolites and proteins.
This document provides a summary of Md. Ariful Islam's background and qualifications. It outlines his education, including pursuing a Ph.D. in Computer Science at Stony Brook University with a focus on modeling, simulation, and formal verification of complex software and dynamical systems. It also lists his skills and experiences in areas such as mathematical modeling, verification and validation, control theory, and statistics.
BioDec, based near Bologna, Italy, provides top-notch services, solutions, and consulting in the field of lab data management and in postgenomics "in silico" research. The presentation summarizes our main achievements and describes our commercial offer.
The Proteomics and Metabolomics Shared Resource (PMSR) at Georgetown University provides proteomics and metabolomics services and expertise. The document describes the PMSR's integrated proteomics workflow including 2D gel-based analysis, DIGE, spot picking, and MALDI TOF/TOF mass spectrometry for protein identification. Liquid chromatography-based proteomics using iTRAQ/ICAT labeling for quantitative analysis and a nano LC-QSTAR ELITE mass spectrometer are also described. The PMSR supports small molecule profiling and quantitation using UPLC-TOFMS and metabolomics applications.
Rashad Badrawi has training in biological and computer sciences. He has a BS in Biology, MS degrees in Pharmacology and Information Systems. He has worked as a software engineer and bioinformatics specialist at several universities and companies. Some of his projects include building GeneMania's data warehouse, translating the BIND interactions database, and designing interoperability between Virtual Cell and systems biology standards. His strengths include being a self-starter, team player, and mentor who enjoys building products from start to finish while keeping up with advances in biomedical informatics.
Amol Ashok Kunde is seeking a position in neurology development. He has a Master's in Computational biology and 1.5 years of research experience. His experience includes molecular biology techniques, using drug discovery software, and working as an assistant manager. He has experience designing automated pipelines for analysis, classifying brain tumors using neural networks, and insilico drug design.
Artificial Intelligence and Machine Learning Operated Pesticide SprayerIRJET Journal
The document describes the development of an artificially intelligent and machine learning operated pesticide sprayer. The sprayer uses computer vision to identify healthy and unhealthy plant leaves and only sprays pesticides on leaves that require treatment. This helps reduce overuse of pesticides, saves time and labor for farmers, and protects soil health. The sprayer is designed with a raspberry pi microcontroller that controls actuators like motors and pumps. Machine learning algorithms are trained on image datasets to recognize healthy and unhealthy leaves, and the sprayer is programmed to actuate pesticide spraying accordingly. The system aims to automate pesticide application in agriculture for improved accuracy, efficiency and reduced human effort.
Pharma Research Automation by Connecting Researchers with Robots and Systems ...camunda services GmbH
The discovery of new therapeutic molecule has become a highly demanding endeavour. The main goal is to find an effective molecule, i.e. one that address a particular disease. On this path many conditions need to be met. A critical one is to ensure the safety of the molecule, meaning that it only targets the disease and nothing more. Next, while having ensured safety and effectiveness, another question that arises is the suitability for production, i.e. is it even possible to produce the molecule consistently and at scale over the many years the medicine will be available on the market? This is especially challenging for biologics, i.e. large therapeutic molecules produced by living cells.
Looking at the software landscape in pharma research we are confronted with a highly heterogeneous view, involving a broad combinations of different software systems with various interfacing possibilities. Molecules are tracked in registration systems, lab information management systems or electronic lab notebooks store process data. Requests between labs are handled by requesting systems, robotic systems (liquid handlers, analytics) produce large data and we can’t ignore the amount of spreadsheets used to document or calculate.
While faced with complex questions, researchers have developed a series of individual methods that, on their own, answer or help with a small part of the questions above. The true value comes by automating the combination of these methods into end-to-end processes that answer the full research question. Thus it is more than fitting to use business process modelling not only to describe the research process, but to also execute it.
In this presentation we show the use of business process modelling to map and drive research processes stretching over researcher decision points, backend systems and robots. In particular, our current robot integration is to treat robots as external systems where the orchestration engine configures, monitors and collects results while the user is still fully in charge of loading and triggering an actual run. Unlike fully automated setups, a research environment demands flexibility as processes and their branches change. Even so, we show by using executable business processes in the pharma industry research, we increase throughput, transparency, standardization and time-to-results .
This document provides a summary of Md. Ariful Islam's background and qualifications. He is a PhD candidate in Computer Science at Stony Brook University focused on modeling, simulation, and formal verification of complex software and dynamical systems. He has extensive skills in various modeling, simulation, optimization, and programming languages and tools.
SooryaKiran Bioinformatics is a global bioinformatics solutions provider that focuses on customized bioinformatics services and products. It develops algorithms and software for biological sequence analysis, structure prediction, and other areas. Key products include tools for sequence generation, analysis, and homology identification. The company collaborates with research institutions and has provided solutions for SNP analysis, genome analysis, and mitochondrial DNA analysis to clients around the world.
This document discusses molecular modelling and docking techniques. It describes molecular docking as a computational method to predict how two molecules, such as a protein and ligand, interact and bind with each other. It outlines key stages in docking like receptor and ligand selection and preparation. It also discusses different docking tools, types of docking including rigid and flexible docking, scoring functions used to evaluate predicted complexes, and examples of specific enzymes like dihydrofolate reductase that can be modeled.
Emerging Challenges for Artificial Intelligence in Medicinal ChemistryEd Griffen
Presentation by Dr Ed Griffen of MedChemica Ltd, at The IBSA Conference "How Artificial Intelligence Can Change the Pharmaceutical Landscape“ - LUGANO, October 9th 2019.
- Suraj S Hanchate is seeking a position as an Oracle Database Administrator with over 5 years of experience in installing, configuring, and maintaining Oracle databases.
- He has extensive experience with Oracle 10g, 11g, and 12c databases and has worked on projects for electricity departments in Bangalore, Goa, and Jaipur.
- His responsibilities have included database backups, patching, performance tuning, and troubleshooting administration issues.
1) The document discusses integrating OpenClinica, an open-source clinical data management system, with a patient monitoring tool (PMT) to improve efficiency in clinical data management for studies conducted by DNDi and PHPT.
2) Key objectives of the integration are to reduce the time to obtain clean study data sets and decrease error rates by facilitating real-time monitoring of patient data entered into OpenClinica.
3) The methodology developed uses a community data mart to transfer study data from OpenClinica to the PMT database, allowing monitors to access collated subject data through a single interface and improving monitoring.
Protein structure-based design and engineering can provide insights into protein function and improve protein properties through molecular modelling and targeted mutations. Molecular modelling generates 3D protein structures from sequences to understand structure-function relationships and identify active sites, domains, and other structural features. It also enables large-scale in silico mutation screening to focus experimental efforts on the most promising recombinant protein variants for applications in health, environment, and technology.
DNA Query Language DNAQL: A Novel ApproachEditor IJCATR
This document describes a proposed DNA Query Language (DNAQL) that could allow researchers to query DNA databases in a more intuitive way compared to SQL. The DNAQL is presented as a novel approach that would introduce an abstraction layer between the user interface and database, translating queries in a familiar biochemical language into SQL understood by the database. This could help alleviate challenges biochemistry researchers face in accessing and analyzing protein data from databases. The document provides background on DNA computing and challenges in current databases, reviews related work on biological database querying, and describes the proposed methodology for DNA sequencing and DNAQL.
This document summarizes the services provided by an organization that conducts research and training in areas related to biotechnology and pharmaceuticals. They provide online and in-person training programs and research projects in topics such as bioinformatics, drug design, genomics, and proteomics. They have completed over 20 research projects in the past year that have led to international publications. They also organize workshops on drug discovery and genomics at universities and institutions around the world, both in-person and online. Their goal is to strengthen the skills and careers of young researchers through hands-on training and research experience.
A systematic review of network analyst - PubricaPubrica
In a Systematic Review Writing, the network analyst is a bioinformatics tool designed to perform efficient PPI network analysis for data generated from gene expression experiments the following contents explain about the network analyst and their methods, in brief, using the help of Pubrica blog.
Continue Reading: https://bit.ly/3nAa3ek
Reference: https://pubrica.com/services/research-services/systematic-review/
Why Pubrica?
When you order our services, Plagiarism free|on Time|outstanding customer support|Unlimited Revisions support|High-quality Subject Matter Experts.
Contact us :
Web: https://pubrica.com/
Blog: https://pubrica.com/academy/
Email: sales@pubrica.com
WhatsApp : +91 9884350006
United Kingdom: +44- 74248 10299
This document provides an overview of biotechnology and bioinformatics for students. It discusses the main branches of biotechnology including microbiology, biochemistry, cell biology, and bioinformatics. Bioinformatics is defined as involving bio data storage, sequence analysis, and computer aided drug design. Molecular docking is described as a process to determine the compatibility of two molecules like a lock and key through binding of ligands and proteins. The document outlines the steps in molecular docking, types of docking, and softwares used. Finally, it discusses several important biological databases used in bioinformatics research including NCBI, SwissADME, DrugBank, and PDB.
This document provides information about the Metabolic Engineering course taught by Dr. Lovely at Noida Institute of Engineering and Technology. It includes details about the course syllabus, units covered, evaluation scheme, course objectives and outcomes. The key topics covered are metabolic flux analysis, experimental determination of metabolic fluxes, computational modelling of biological networks, and industrial applications of metabolic engineering including pathway engineering strategies for production of commercially important metabolites and proteins.
This document provides a summary of Md. Ariful Islam's background and qualifications. It outlines his education, including pursuing a Ph.D. in Computer Science at Stony Brook University with a focus on modeling, simulation, and formal verification of complex software and dynamical systems. It also lists his skills and experiences in areas such as mathematical modeling, verification and validation, control theory, and statistics.
BioDec, based near Bologna, Italy, provides top-notch services, solutions, and consulting in the field of lab data management and in postgenomics "in silico" research. The presentation summarizes our main achievements and describes our commercial offer.
The binding of cosmological structures by massless topological defectsSérgio Sacani
Assuming spherical symmetry and weak field, it is shown that if one solves the Poisson equation or the Einstein field
equations sourced by a topological defect, i.e. a singularity of a very specific form, the result is a localized gravitational
field capable of driving flat rotation (i.e. Keplerian circular orbits at a constant speed for all radii) of test masses on a thin
spherical shell without any underlying mass. Moreover, a large-scale structure which exploits this solution by assembling
concentrically a number of such topological defects can establish a flat stellar or galactic rotation curve, and can also deflect
light in the same manner as an equipotential (isothermal) sphere. Thus, the need for dark matter or modified gravity theory is
mitigated, at least in part.
Travis Hills' Endeavors in Minnesota: Fostering Environmental and Economic Pr...Travis Hills MN
Travis Hills of Minnesota developed a method to convert waste into high-value dry fertilizer, significantly enriching soil quality. By providing farmers with a valuable resource derived from waste, Travis Hills helps enhance farm profitability while promoting environmental stewardship. Travis Hills' sustainable practices lead to cost savings and increased revenue for farmers by improving resource efficiency and reducing waste.
The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptxMAGOTI ERNEST
Although Artemia has been known to man for centuries, its use as a food for the culture of larval organisms apparently began only in the 1930s, when several investigators found that it made an excellent food for newly hatched fish larvae (Litvinenko et al., 2023). As aquaculture developed in the 1960s and ‘70s, the use of Artemia also became more widespread, due both to its convenience and to its nutritional value for larval organisms (Arenas-Pardo et al., 2024). The fact that Artemia dormant cysts can be stored for long periods in cans, and then used as an off-the-shelf food requiring only 24 h of incubation makes them the most convenient, least labor-intensive, live food available for aquaculture (Sorgeloos & Roubach, 2021). The nutritional value of Artemia, especially for marine organisms, is not constant, but varies both geographically and temporally. During the last decade, however, both the causes of Artemia nutritional variability and methods to improve poorquality Artemia have been identified (Loufi et al., 2024).
Brine shrimp (Artemia spp.) are used in marine aquaculture worldwide. Annually, more than 2,000 metric tons of dry cysts are used for cultivation of fish, crustacean, and shellfish larva. Brine shrimp are important to aquaculture because newly hatched brine shrimp nauplii (larvae) provide a food source for many fish fry (Mozanzadeh et al., 2021). Culture and harvesting of brine shrimp eggs represents another aspect of the aquaculture industry. Nauplii and metanauplii of Artemia, commonly known as brine shrimp, play a crucial role in aquaculture due to their nutritional value and suitability as live feed for many aquatic species, particularly in larval stages (Sorgeloos & Roubach, 2021).
The ability to recreate computational results with minimal effort and actionable metrics provides a solid foundation for scientific research and software development. When people can replicate an analysis at the touch of a button using open-source software, open data, and methods to assess and compare proposals, it significantly eases verification of results, engagement with a diverse range of contributors, and progress. However, we have yet to fully achieve this; there are still many sociotechnical frictions.
Inspired by David Donoho's vision, this talk aims to revisit the three crucial pillars of frictionless reproducibility (data sharing, code sharing, and competitive challenges) with the perspective of deep software variability.
Our observation is that multiple layers — hardware, operating systems, third-party libraries, software versions, input data, compile-time options, and parameters — are subject to variability that exacerbates frictions but is also essential for achieving robust, generalizable results and fostering innovation. I will first review the literature, providing evidence of how the complex variability interactions across these layers affect qualitative and quantitative software properties, thereby complicating the reproduction and replication of scientific studies in various fields.
I will then present some software engineering and AI techniques that can support the strategic exploration of variability spaces. These include the use of abstractions and models (e.g., feature models), sampling strategies (e.g., uniform, random), cost-effective measurements (e.g., incremental build of software configurations), and dimensionality reduction methods (e.g., transfer learning, feature selection, software debloating).
I will finally argue that deep variability is both the problem and solution of frictionless reproducibility, calling the software science community to develop new methods and tools to manage variability and foster reproducibility in software systems.
Exposé invité Journées Nationales du GDR GPL 2024
Authoring a personal GPT for your research and practice: How we created the Q...Leonel Morgado
Thematic analysis in qualitative research is a time-consuming and systematic task, typically done using teams. Team members must ground their activities on common understandings of the major concepts underlying the thematic analysis, and define criteria for its development. However, conceptual misunderstandings, equivocations, and lack of adherence to criteria are challenges to the quality and speed of this process. Given the distributed and uncertain nature of this process, we wondered if the tasks in thematic analysis could be supported by readily available artificial intelligence chatbots. Our early efforts point to potential benefits: not just saving time in the coding process but better adherence to criteria and grounding, by increasing triangulation between humans and artificial intelligence. This tutorial will provide a description and demonstration of the process we followed, as two academic researchers, to develop a custom ChatGPT to assist with qualitative coding in the thematic data analysis process of immersive learning accounts in a survey of the academic literature: QUAL-E Immersive Learning Thematic Analysis Helper. In the hands-on time, participants will try out QUAL-E and develop their ideas for their own qualitative coding ChatGPT. Participants that have the paid ChatGPT Plus subscription can create a draft of their assistants. The organizers will provide course materials and slide deck that participants will be able to utilize to continue development of their custom GPT. The paid subscription to ChatGPT Plus is not required to participate in this workshop, just for trying out personal GPTs during it.
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...Leonel Morgado
Current descriptions of immersive learning cases are often difficult or impossible to compare. This is due to a myriad of different options on what details to include, which aspects are relevant, and on the descriptive approaches employed. Also, these aspects often combine very specific details with more general guidelines or indicate intents and rationales without clarifying their implementation. In this paper we provide a method to describe immersive learning cases that is structured to enable comparisons, yet flexible enough to allow researchers and practitioners to decide which aspects to include. This method leverages a taxonomy that classifies educational aspects at three levels (uses, practices, and strategies) and then utilizes two frameworks, the Immersive Learning Brain and the Immersion Cube, to enable a structured description and interpretation of immersive learning cases. The method is then demonstrated on a published immersive learning case on training for wind turbine maintenance using virtual reality. Applying the method results in a structured artifact, the Immersive Learning Case Sheet, that tags the case with its proximal uses, practices, and strategies, and refines the free text case description to ensure that matching details are included. This contribution is thus a case description method in support of future comparative research of immersive learning cases. We then discuss how the resulting description and interpretation can be leveraged to change immersion learning cases, by enriching them (considering low-effort changes or additions) or innovating (exploring more challenging avenues of transformation). The method holds significant promise to support better-grounded research in immersive learning.
The debris of the ‘last major merger’ is dynamically youngSérgio Sacani
The Milky Way’s (MW) inner stellar halo contains an [Fe/H]-rich component with highly eccentric orbits, often referred to as the
‘last major merger.’ Hypotheses for the origin of this component include Gaia-Sausage/Enceladus (GSE), where the progenitor
collided with the MW proto-disc 8–11 Gyr ago, and the Virgo Radial Merger (VRM), where the progenitor collided with the
MW disc within the last 3 Gyr. These two scenarios make different predictions about observable structure in local phase space,
because the morphology of debris depends on how long it has had to phase mix. The recently identified phase-space folds in Gaia
DR3 have positive caustic velocities, making them fundamentally different than the phase-mixed chevrons found in simulations
at late times. Roughly 20 per cent of the stars in the prograde local stellar halo are associated with the observed caustics. Based
on a simple phase-mixing model, the observed number of caustics are consistent with a merger that occurred 1–2 Gyr ago.
We also compare the observed phase-space distribution to FIRE-2 Latte simulations of GSE-like mergers, using a quantitative
measurement of phase mixing (2D causticality). The observed local phase-space distribution best matches the simulated data
1–2 Gyr after collision, and certainly not later than 3 Gyr. This is further evidence that the progenitor of the ‘last major merger’
did not collide with the MW proto-disc at early times, as is thought for the GSE, but instead collided with the MW disc within
the last few Gyr, consistent with the body of work surrounding the VRM.
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...Sérgio Sacani
Context. With a mass exceeding several 104 M⊙ and a rich and dense population of massive stars, supermassive young star clusters
represent the most massive star-forming environment that is dominated by the feedback from massive stars and gravitational interactions
among stars.
Aims. In this paper we present the Extended Westerlund 1 and 2 Open Clusters Survey (EWOCS) project, which aims to investigate
the influence of the starburst environment on the formation of stars and planets, and on the evolution of both low and high mass stars.
The primary targets of this project are Westerlund 1 and 2, the closest supermassive star clusters to the Sun.
Methods. The project is based primarily on recent observations conducted with the Chandra and JWST observatories. Specifically,
the Chandra survey of Westerlund 1 consists of 36 new ACIS-I observations, nearly co-pointed, for a total exposure time of 1 Msec.
Additionally, we included 8 archival Chandra/ACIS-S observations. This paper presents the resulting catalog of X-ray sources within
and around Westerlund 1. Sources were detected by combining various existing methods, and photon extraction and source validation
were carried out using the ACIS-Extract software.
Results. The EWOCS X-ray catalog comprises 5963 validated sources out of the 9420 initially provided to ACIS-Extract, reaching a
photon flux threshold of approximately 2 × 10−8 photons cm−2
s
−1
. The X-ray sources exhibit a highly concentrated spatial distribution,
with 1075 sources located within the central 1 arcmin. We have successfully detected X-ray emissions from 126 out of the 166 known
massive stars of the cluster, and we have collected over 71 000 photons from the magnetar CXO J164710.20-455217.
The technology uses reclaimed CO₂ as the dyeing medium in a closed loop process. When pressurized, CO₂ becomes supercritical (SC-CO₂). In this state CO₂ has a very high solvent power, allowing the dye to dissolve easily.
2. What are the hardware and software
requirements to run molecular
docking?
01. MD Requirements
What is the biological question to be
answered by employing MD in this
tutorial?
02.
Project Design
What are the factors to consider when
choosing molecular docking
program(s)?
03.
Molecular Docking Program
Selection
What are the steps involved in
computing for molecular docking?
04. Molecular Docking Steps
Contents
4. ● Computers with fast processors and plenty of
memory.
● Multi-core CPU with at least 8GB of RAM is
recommended,
● The computer should have graphics processing unit
(GPU) with high computational power.
Hardware
5. ● Access to structures databases e.g PDB RCSB,
PDBj, PDBe, uniprot, NCBI(Genebank), Alphafold,
Pubchem, ChemBL, Chemspider, ZINC, Drugbank
etc.
● Molecular docking software packages /webservers
e.g AutoDock, AutoDock Vina, GOLD, Glide, PyRx,
Swissdock, playmolecule etc.
● Software/web tools for data preparation,
visualization, and analysis of the results e.g PyMOL
or Chimera, Discovery Studio Visualizer, OpenBabel,
DataWarrior, playmolecule, Cytoscape etc.
Software
8. Project Design
What is the biological question to be answered
by employing MD in this tutorial ?
9. This project aims to assess and
evaluate the efficacy of
phytocompounds present in Moringa
Oleifera aqueous and methanolic
extracts in the treatment of
parkinson’s disease(PD) by targeting
a pool of protein targets implicated
in PD.
Exploring the Neuroprotective Properties of Moringa Oleifera: Insights
from Molecular Docking Studies with Parkinson's Disease Protein Targets
N.B: This is the official project for this workshop.
11. MD
STEPS
STEP 02. Protein Retrieval
STEP 01. Protein Identification
STEP 04. Ligand Identification
STEP 03. Protein Preparation
Understanding implicated protein(s) structure,
working dynamics and biochemical interactions.
Download of protein structure from protein data
banks.
Removal of unwanted parameters, addition of
necessary parameters and structure
optimization.
Knowledge about the ligand/compound(s) of
study.
12. MD
STEPS
Necessary ligand modifications and
optimization.
STEP 06. Ligand Preparation
Download of ligand structure from
compound databases.
STEP 05. Ligand Retrieval
Analysis of the docking poses and
interactions.
STEP 08. Docking Result Analysis
Docking computation by employing
docking programs.
STEP 07. Docking
STEP 09. Pharmacokinetic Screening
STEP 10. Validation
ADME and toxicity screening of hit
ligands
Evaluation of docking predictions
accuracy and reliability.