This document summarizes an undergraduate final year project that developed a protein quantification pipeline using top-down proteomics to analyze heavy metal contamination in Hudiara Drain in Lahore, Pakistan. The project aimed to identify specific proteins responsible for fixing each heavy metal to enable better bioremediation of the drain. It proposed developing a mass spectrometry data analysis platform using GPUs and algorithms for theoretical pattern generation, spectrum deconvolution, peak extraction, and protein quantification. The platform was implemented as a web service to analyze microbial protein content and quantify amounts needed for substantial bioremediation of Hudiara Drain and other environments.
EUGM 2014 - Richard Bolton (GlaxoSmithKline): GlaxoSmithKline: 5 years with ...ChemAxon
GlaxoSmithKline began using ChemAxon tools across its enterprise systems in late 2009. A selection of presentations from previous UGM which reflect the increasing usage and show the developing relationship between the two companies will be highlighted and key status updated. A new use for ChemAxon tools in Enterprise Search will be presented.
The document discusses research information management processes and the CERIFY project. It describes mapping current 'as is' processes and identifying gaps to develop improved 'to be' processes using CERIF. Specific areas discussed include developing CERIF data models and processes for exchanging data with Thomson Reuters' InCites system and for capturing measures of esteem. The goal is to standardize data through authority lists and taxonomies to make the processes more efficient and help verify information.
The CompTox Chemistry Dashboard was developed by the Environmental Protection Agency’s National Center for Computational Toxicology. This dashboard has been architected in a manner that allows for the deployment of multiple “applications”, both as publicly available databases, and for deployment under the constraints of confidential business information (CBI). The public dashboard provide access to multiple types of data for ~750,000 chemicals. This includes, when available for a chemical substance, physicochemical parameters, toxicity and bioassay data, consumer use and analytical data. Fate, exposure, and hazard calculations can benefit from access to the data aggregation and curation efforts that underpin the public dashboard. Also, regulators can benefit from the integration of their own data within their closed infrastructure environments. This presentation will provide a review of the chemistry dashboard architecture and its present application providing access to data to the research and regulatory communities. We will also review present developments in the area of delivering an application programming interface, web services, and software components for integration into third party applications providing access to the data exposed via the dashboard. This abstract does not reflect U.S. EPA policy.
The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrate advances in biology, chemistry, exposure and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. As an outcome of these efforts the National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences including high-throughput in vitro screening data, legacy in vivo animal data, consumer use and production information, exposure models and chemical structure databases with associated properties. A series of software applications and databases have been produced over the past decade to deliver these data, but recent developments have focused on the development of a new software architecture that assembles the resources into a single platform. Our web application, the CompTox Chemistry Dashboard provides access to data associated with ~750,000 chemical substances. These data include experimental and predicted physicochemical property data, bioassay screening data associated with the ToxCast program, product and functional use information and a myriad of related data of value to environmental scientists.
The dashboard provides chemical-based searching based on chemical names, synonyms and CAS Registry Numbers. Flexible search capabilities allow for chemical identification based on non-targeted analysis studies using mass spectrometry. Chemical identification using both mass and formula-based searching utilizes rank-ordering of results via functional use statistics, thereby providing a solution to help prioritize chemicals for further review when detected in environmental media.
This presentation will provide an overview of the dashboard, its capabilities for delivering data to the environmental chemistry community and how the architecture provides a foundation for the development of additional applications to support chemical risk assessment. This abstract does not reflect U.S. EPA policy.
Introduction to the Purdue Agile Strategy Lab January 2019Ed Morrison
This presentation gives you an overview of the activities of the Purdue Agile Strategy Lab. We developed Strategic Doing, an open source operating system for collaboration, open innovation and ecosystem development.
We also work closely with Fraunhofer IAO on innovation and technology management and with Human Insight, a Dutch firm that focuses on cognitive diversity in teams.
Hang Su is seeking a full-time position as a Mechanical Engineer starting in summer 2016. She is graduating in May 2016 with a Master's degree in Mechanical Engineering from Arizona State University, specializing in radiation heat transfer, thermodynamics, and microelectronic packaging. She has internship experience in manufacturing and has worked on projects involving CAD modeling, optoelectronics, and heat transfer simulation.
Approach and outcome of the Biodiversity Virtual e-Laboratory (BioVeL) projectAlex Hardisty
The document summarizes the BioVeL project, which created a biodiversity virtual e-laboratory infrastructure. It discusses (1) the background and objectives of providing web services and workflows for cross-disciplinary biodiversity analysis, (2) the key achievements including 50 services, several workflow families, and an operational virtual laboratory portal, and (3) lessons learned regarding focusing on high-value assets, better promoting the project, and addressing scalability challenges.
This document summarizes an undergraduate final year project presentation on wireless power transmission using magnetic resonance. A team of three electrical engineering students from the University of Engineering and Technology Lahore presented their work. Their proposed solution was to use magnetic resonance for wireless power transmission without wires. They discussed their block diagram, hardware developed including a Tesla coil prototype, tests performed, future plans, and references. The goal of the project was to research and demonstrate wireless power transmission over distance without wires.
EUGM 2014 - Richard Bolton (GlaxoSmithKline): GlaxoSmithKline: 5 years with ...ChemAxon
GlaxoSmithKline began using ChemAxon tools across its enterprise systems in late 2009. A selection of presentations from previous UGM which reflect the increasing usage and show the developing relationship between the two companies will be highlighted and key status updated. A new use for ChemAxon tools in Enterprise Search will be presented.
The document discusses research information management processes and the CERIFY project. It describes mapping current 'as is' processes and identifying gaps to develop improved 'to be' processes using CERIF. Specific areas discussed include developing CERIF data models and processes for exchanging data with Thomson Reuters' InCites system and for capturing measures of esteem. The goal is to standardize data through authority lists and taxonomies to make the processes more efficient and help verify information.
The CompTox Chemistry Dashboard was developed by the Environmental Protection Agency’s National Center for Computational Toxicology. This dashboard has been architected in a manner that allows for the deployment of multiple “applications”, both as publicly available databases, and for deployment under the constraints of confidential business information (CBI). The public dashboard provide access to multiple types of data for ~750,000 chemicals. This includes, when available for a chemical substance, physicochemical parameters, toxicity and bioassay data, consumer use and analytical data. Fate, exposure, and hazard calculations can benefit from access to the data aggregation and curation efforts that underpin the public dashboard. Also, regulators can benefit from the integration of their own data within their closed infrastructure environments. This presentation will provide a review of the chemistry dashboard architecture and its present application providing access to data to the research and regulatory communities. We will also review present developments in the area of delivering an application programming interface, web services, and software components for integration into third party applications providing access to the data exposed via the dashboard. This abstract does not reflect U.S. EPA policy.
The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrate advances in biology, chemistry, exposure and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. As an outcome of these efforts the National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences including high-throughput in vitro screening data, legacy in vivo animal data, consumer use and production information, exposure models and chemical structure databases with associated properties. A series of software applications and databases have been produced over the past decade to deliver these data, but recent developments have focused on the development of a new software architecture that assembles the resources into a single platform. Our web application, the CompTox Chemistry Dashboard provides access to data associated with ~750,000 chemical substances. These data include experimental and predicted physicochemical property data, bioassay screening data associated with the ToxCast program, product and functional use information and a myriad of related data of value to environmental scientists.
The dashboard provides chemical-based searching based on chemical names, synonyms and CAS Registry Numbers. Flexible search capabilities allow for chemical identification based on non-targeted analysis studies using mass spectrometry. Chemical identification using both mass and formula-based searching utilizes rank-ordering of results via functional use statistics, thereby providing a solution to help prioritize chemicals for further review when detected in environmental media.
This presentation will provide an overview of the dashboard, its capabilities for delivering data to the environmental chemistry community and how the architecture provides a foundation for the development of additional applications to support chemical risk assessment. This abstract does not reflect U.S. EPA policy.
Introduction to the Purdue Agile Strategy Lab January 2019Ed Morrison
This presentation gives you an overview of the activities of the Purdue Agile Strategy Lab. We developed Strategic Doing, an open source operating system for collaboration, open innovation and ecosystem development.
We also work closely with Fraunhofer IAO on innovation and technology management and with Human Insight, a Dutch firm that focuses on cognitive diversity in teams.
Hang Su is seeking a full-time position as a Mechanical Engineer starting in summer 2016. She is graduating in May 2016 with a Master's degree in Mechanical Engineering from Arizona State University, specializing in radiation heat transfer, thermodynamics, and microelectronic packaging. She has internship experience in manufacturing and has worked on projects involving CAD modeling, optoelectronics, and heat transfer simulation.
Approach and outcome of the Biodiversity Virtual e-Laboratory (BioVeL) projectAlex Hardisty
The document summarizes the BioVeL project, which created a biodiversity virtual e-laboratory infrastructure. It discusses (1) the background and objectives of providing web services and workflows for cross-disciplinary biodiversity analysis, (2) the key achievements including 50 services, several workflow families, and an operational virtual laboratory portal, and (3) lessons learned regarding focusing on high-value assets, better promoting the project, and addressing scalability challenges.
This document summarizes an undergraduate final year project presentation on wireless power transmission using magnetic resonance. A team of three electrical engineering students from the University of Engineering and Technology Lahore presented their work. Their proposed solution was to use magnetic resonance for wireless power transmission without wires. They discussed their block diagram, hardware developed including a Tesla coil prototype, tests performed, future plans, and references. The goal of the project was to research and demonstrate wireless power transmission over distance without wires.
This document provides a final progress report for research project 247099, a collaboration between the Universidad Michoacana de San Nicolás de Hidalgo in Mexico and the University of Strathclyde in the UK. The project aims to study harmonic power flows, power quality estimation, and techniques for mitigating harmonic distortion. To date, the collaboration has produced journal papers, conference presentations, and supervised doctoral students. Pending activities include further research visits and the preparation of final reports on the findings and impact of strengthening ties between the two institutions.
The European Open Science Cloud: just what is it?Carole Goble
Presented at Jisc and CNI leaders conference 2018, 2 July 2018, Oxford, UK (https://www.jisc.ac.uk/events/jisc-and-cni-leaders-conference-02-jul-2018). The European Open Science Cloud. What exactly is it? In principle it is conceived as a virtual environment with open and seamless services for storage, management, analysis and re-use of research data, across borders and scientific disciplines. How? By federating existing scientific data infrastructures, currently dispersed across disciplines and Member States. In practice, what it is depends on the stakeholder. To European Research Infrastructures it’s a coordinated mission to organise and exchange their data, metadata, software and services to be FAIR – Findable, Accessible, Interoperable, Reusable – and to use e-Infrastructures, either EU or commercial. To EU e-Infrastructures offering data storage and cloud services, it’s a funding mission to integrate their services, policies and organisational structures, and to be used by the Research Infrastructures. To agencies it’s a means to promote Open Science, standardisation, cross-disciplinary research and coordinated investment with a dream of a “one stop shop” for researchers. And for Libraries?
The document provides an overview of research data management for the School of Engineering at the University of Lincoln. It discusses the benefits of research data management, including increased transparency, collaboration, and opportunities for new research. It also outlines some of the support and requirements for research data management from funders and institutions.
SOPHIA by Philippe Malbranch - Maghrenov workshop on research infrastructures...Maghrenov
The document summarizes the SOPHIA project which aimed to promote coordination among PV research infrastructures in Europe. The project involved 17 research organizations and 3 associations. It had three main activities: 1) Providing transnational access to 48 research facilities for 56 proposals, 2) Improving research infrastructure services through joint activities like benchmarking and validation, 3) Networking activities including workshops, databases and a strategic research agenda. The project concluded that increased coordination can provide better value through actions like harmonizing characterization, benchmarking, training and mutual access to infrastructures.
Modelling of Multi-Scale Phenomena in Nano-SuspensionsEUDAT
This document summarizes research using multi-scale modeling and simulations to understand phenomena in nano-suspensions. It discusses (1) motivations for studying nano-suspensions for applications like biomedical, mechanical, chemical, and energy uses; (2) the multi-scale modeling approach using molecular dynamics and Brownian dynamics; (3) use of HPC facilities through PRACE and data management with EUDAT; (4) results on potential of mean force and hydration layers; and (5) perspectives on self-assembly of patchy nanoparticles and importance of managing data with EUDAT.
The document summarizes a presentation on assessing the global gas research and development (R&D) outlook using patent analytics. It analyzes gas-related patents from six major intellectual property offices between 2004-2014. The results show polarizing R&D landscapes across different segments of the gas chain, with exploration and production seeing disruptive growth while other segments saw more incremental advances or declining interest. Overall R&D needs to move beyond short-term drivers in exploration/production to long-term economic and social value, and increase collaboration between segments and industries to consolidate resources and shorten R&D lifecycles.
This project aims to develop new nanoporous carbonaceous materials from renewable resources like starch as a sustainable alternative to fossil fuels. The project receives funding from the European Union and involves nine partners across Europe. It seeks to refine the production process from research to an industrial pilot plant capable of producing 20kg per day of material for applications in energy storage, catalysis, and other industrial uses.
The document proposes the development of piezoresistive transistors using layered dichalcogenide materials to overcome limitations in silicon-based devices. It outlines a 3-phase technical approach to optimize materials, demonstrate a large-scale functional prototype, and develop a full-scale prototype. A project timeline, budget, and potential economic and social impacts are also presented.
This document discusses developing the next generation of completion engineers through advanced engineering training. It defines the need for such training by highlighting workforce gaps, global expansion of unconventionals, and the multidisciplinary knowledge required. Training options presented include internally-focused engineering programs and using industry resources from SPE. Companies that focus on advanced training will have a more competent workforce.
This document summarizes an undergraduate final year project presentation on developing a laboratory workbench for partial discharge measurement of electrical equipment. A team of four electrical engineering students presented their work on designing and building equipment to detect partial discharges, which can indicate insulation issues in transformers and other high-voltage devices. They proposed using acoustic sensors to detect partial discharge signals and developed simulations, hardware, and plans for further study on applying their technique to other power equipment.
This document summarizes an undergraduate final year project presentation on developing a laboratory workbench for partial discharge measurement of electrical equipment. A team of four electrical engineering students presented their work on designing and building equipment to detect partial discharges, which can indicate insulation issues in transformers and other high-voltage devices. They proposed using acoustic sensors to detect partial discharge signals and developed simulations, hardware, and plans for further study on applying their technique to other power equipment.
UK HE Research Data Management Survey Results - Presentation to EPSRCMartin Hamilton
We recently surveyed UK Higher Education Institutions on their plans for Research Data Management (RDM) to inform our own RDM project - the results can be found on my blog at http://martinh.net. These slides are a summary of the results which we presented to EPSRC in November 2013.
This presentation is a brief description of our international project on Utility Services.
This project deals with Big Data, Open Data, R analytics.
Universities and Industry working together sharing knowledge and expertise.
Only by private funding by the moment.
Knowledge and technology transfer is our main goal.
Slides from March1st 2018 webinar
Tracking research data footprints via integration with Research Graph
Presented by Ben Evans and Jingbo Wang from NCI
Benchmarking Commercial RDF Stores with Publications Office DatasetGhislain Atemezing
The slides present a benchmark of RDF stores with real-world datasets and queries from the EU Publications Office (PO). The study compares the performance of four commercial triple stores: Stardog 4.3 EE, GraphDB 8.0.3 EE, Oracle 12.2c and Virtuoso 7.2.4.2 with respect to the following requirements: bulk loading, scalability, stability and query execution.
Horizon Europe Clean Energy Webinar - Cluster 5 Destination 3 | PitchesKTN
This webinar highlights funding call topics within Cluster 5 / Destination 3 of the Horizon Europe Framework Programme and bring you plenty of networking opportunities.
The European Open Science Cloud: just what is it?Jisc
The European Open Science Cloud (EOSC) aims to provide a virtual environment for Europe's 1.7 million researchers to store, share, and reuse research outputs. It will reduce duplication of efforts and simplify access across borders and disciplines. The EOSC will be guided by FAIR principles to make data findable, accessible, interoperable, and reusable. Its implementation will focus on engaging stakeholders, developing open standards and interoperable services, and addressing skills gaps in data management. The EOSC seeks to build on existing research infrastructures and e-infrastructures through a distributed and community-driven approach.
Microfluidic Flow Control using Magnetohydrodynamics KayDrive
Fluid manipulation in microfluidic devices is one of the main areas of research interest for the fabrication of Lab-On-a-Chip devices. From the many methods that have been applied to this problem, one of the most promising is employing Magnetohydrodynamic principles which allow for elegant and versatile designs. A microchip is designed for fluid flow control that uses MHD for pumping the fluid through a microchannel. Simulation of the design is performed in COMSOL and the velocity profile of the fluid is obtained. The microchip is fabricated, and experiments are performed by measuring the flow rate of a conducting fluid as it is pumped by the Lorentz force. The experimental results are then compared with the simulation results to compare the performance of the device to theoretical computations.
The main objective of this project is to advance the local merchants, by creating a community where people can share their meaningful experiences and help each other find the best option available out there, saving time and money.
This document provides a final progress report for research project 247099, a collaboration between the Universidad Michoacana de San Nicolás de Hidalgo in Mexico and the University of Strathclyde in the UK. The project aims to study harmonic power flows, power quality estimation, and techniques for mitigating harmonic distortion. To date, the collaboration has produced journal papers, conference presentations, and supervised doctoral students. Pending activities include further research visits and the preparation of final reports on the findings and impact of strengthening ties between the two institutions.
The European Open Science Cloud: just what is it?Carole Goble
Presented at Jisc and CNI leaders conference 2018, 2 July 2018, Oxford, UK (https://www.jisc.ac.uk/events/jisc-and-cni-leaders-conference-02-jul-2018). The European Open Science Cloud. What exactly is it? In principle it is conceived as a virtual environment with open and seamless services for storage, management, analysis and re-use of research data, across borders and scientific disciplines. How? By federating existing scientific data infrastructures, currently dispersed across disciplines and Member States. In practice, what it is depends on the stakeholder. To European Research Infrastructures it’s a coordinated mission to organise and exchange their data, metadata, software and services to be FAIR – Findable, Accessible, Interoperable, Reusable – and to use e-Infrastructures, either EU or commercial. To EU e-Infrastructures offering data storage and cloud services, it’s a funding mission to integrate their services, policies and organisational structures, and to be used by the Research Infrastructures. To agencies it’s a means to promote Open Science, standardisation, cross-disciplinary research and coordinated investment with a dream of a “one stop shop” for researchers. And for Libraries?
The document provides an overview of research data management for the School of Engineering at the University of Lincoln. It discusses the benefits of research data management, including increased transparency, collaboration, and opportunities for new research. It also outlines some of the support and requirements for research data management from funders and institutions.
SOPHIA by Philippe Malbranch - Maghrenov workshop on research infrastructures...Maghrenov
The document summarizes the SOPHIA project which aimed to promote coordination among PV research infrastructures in Europe. The project involved 17 research organizations and 3 associations. It had three main activities: 1) Providing transnational access to 48 research facilities for 56 proposals, 2) Improving research infrastructure services through joint activities like benchmarking and validation, 3) Networking activities including workshops, databases and a strategic research agenda. The project concluded that increased coordination can provide better value through actions like harmonizing characterization, benchmarking, training and mutual access to infrastructures.
Modelling of Multi-Scale Phenomena in Nano-SuspensionsEUDAT
This document summarizes research using multi-scale modeling and simulations to understand phenomena in nano-suspensions. It discusses (1) motivations for studying nano-suspensions for applications like biomedical, mechanical, chemical, and energy uses; (2) the multi-scale modeling approach using molecular dynamics and Brownian dynamics; (3) use of HPC facilities through PRACE and data management with EUDAT; (4) results on potential of mean force and hydration layers; and (5) perspectives on self-assembly of patchy nanoparticles and importance of managing data with EUDAT.
The document summarizes a presentation on assessing the global gas research and development (R&D) outlook using patent analytics. It analyzes gas-related patents from six major intellectual property offices between 2004-2014. The results show polarizing R&D landscapes across different segments of the gas chain, with exploration and production seeing disruptive growth while other segments saw more incremental advances or declining interest. Overall R&D needs to move beyond short-term drivers in exploration/production to long-term economic and social value, and increase collaboration between segments and industries to consolidate resources and shorten R&D lifecycles.
This project aims to develop new nanoporous carbonaceous materials from renewable resources like starch as a sustainable alternative to fossil fuels. The project receives funding from the European Union and involves nine partners across Europe. It seeks to refine the production process from research to an industrial pilot plant capable of producing 20kg per day of material for applications in energy storage, catalysis, and other industrial uses.
The document proposes the development of piezoresistive transistors using layered dichalcogenide materials to overcome limitations in silicon-based devices. It outlines a 3-phase technical approach to optimize materials, demonstrate a large-scale functional prototype, and develop a full-scale prototype. A project timeline, budget, and potential economic and social impacts are also presented.
This document discusses developing the next generation of completion engineers through advanced engineering training. It defines the need for such training by highlighting workforce gaps, global expansion of unconventionals, and the multidisciplinary knowledge required. Training options presented include internally-focused engineering programs and using industry resources from SPE. Companies that focus on advanced training will have a more competent workforce.
This document summarizes an undergraduate final year project presentation on developing a laboratory workbench for partial discharge measurement of electrical equipment. A team of four electrical engineering students presented their work on designing and building equipment to detect partial discharges, which can indicate insulation issues in transformers and other high-voltage devices. They proposed using acoustic sensors to detect partial discharge signals and developed simulations, hardware, and plans for further study on applying their technique to other power equipment.
This document summarizes an undergraduate final year project presentation on developing a laboratory workbench for partial discharge measurement of electrical equipment. A team of four electrical engineering students presented their work on designing and building equipment to detect partial discharges, which can indicate insulation issues in transformers and other high-voltage devices. They proposed using acoustic sensors to detect partial discharge signals and developed simulations, hardware, and plans for further study on applying their technique to other power equipment.
UK HE Research Data Management Survey Results - Presentation to EPSRCMartin Hamilton
We recently surveyed UK Higher Education Institutions on their plans for Research Data Management (RDM) to inform our own RDM project - the results can be found on my blog at http://martinh.net. These slides are a summary of the results which we presented to EPSRC in November 2013.
This presentation is a brief description of our international project on Utility Services.
This project deals with Big Data, Open Data, R analytics.
Universities and Industry working together sharing knowledge and expertise.
Only by private funding by the moment.
Knowledge and technology transfer is our main goal.
Slides from March1st 2018 webinar
Tracking research data footprints via integration with Research Graph
Presented by Ben Evans and Jingbo Wang from NCI
Benchmarking Commercial RDF Stores with Publications Office DatasetGhislain Atemezing
The slides present a benchmark of RDF stores with real-world datasets and queries from the EU Publications Office (PO). The study compares the performance of four commercial triple stores: Stardog 4.3 EE, GraphDB 8.0.3 EE, Oracle 12.2c and Virtuoso 7.2.4.2 with respect to the following requirements: bulk loading, scalability, stability and query execution.
Horizon Europe Clean Energy Webinar - Cluster 5 Destination 3 | PitchesKTN
This webinar highlights funding call topics within Cluster 5 / Destination 3 of the Horizon Europe Framework Programme and bring you plenty of networking opportunities.
The European Open Science Cloud: just what is it?Jisc
The European Open Science Cloud (EOSC) aims to provide a virtual environment for Europe's 1.7 million researchers to store, share, and reuse research outputs. It will reduce duplication of efforts and simplify access across borders and disciplines. The EOSC will be guided by FAIR principles to make data findable, accessible, interoperable, and reusable. Its implementation will focus on engaging stakeholders, developing open standards and interoperable services, and addressing skills gaps in data management. The EOSC seeks to build on existing research infrastructures and e-infrastructures through a distributed and community-driven approach.
Microfluidic Flow Control using Magnetohydrodynamics KayDrive
Fluid manipulation in microfluidic devices is one of the main areas of research interest for the fabrication of Lab-On-a-Chip devices. From the many methods that have been applied to this problem, one of the most promising is employing Magnetohydrodynamic principles which allow for elegant and versatile designs. A microchip is designed for fluid flow control that uses MHD for pumping the fluid through a microchannel. Simulation of the design is performed in COMSOL and the velocity profile of the fluid is obtained. The microchip is fabricated, and experiments are performed by measuring the flow rate of a conducting fluid as it is pumped by the Lorentz force. The experimental results are then compared with the simulation results to compare the performance of the device to theoretical computations.
The main objective of this project is to advance the local merchants, by creating a community where people can share their meaningful experiences and help each other find the best option available out there, saving time and money.
The gist of our project encapsulates mainly the manufacturing phase of a ring spinning machine.
A ring spinning machine forms threads by isolating individual fibers from yarn, and twisting those fibers co-axially about each other, hence forming a single coalescent thread having been imparted the strength of each fiber.
This project was designed and manufactured locally and the cost was reduced by 78.33% by comparing it with imported machinery.
This document outlines a senior design project for an energy audit and cost analysis of an ammonia plant. The objectives are to understand what an energy audit is, why companies need them, and to analyze the energy efficiency and bottlenecks in Fatima Fertilizers' process. The team will collect plant data, perform calculations and simulations, analyze results, recommend improvements, and conduct a cost analysis. The timeline shows milestones from November 2020 to May 2021. Software like Excel, Polymath, AspenHysys, and MATLAB will be used, along with energy index data from Fatima. Regular communication with industry professionals is also part of the project resources and references.
CodeX is a big data analytics solution that uses novel secure processing and highly efficient data search and analysis techniques. It has a microservices-based architecture in the cloud that offers unique services to Fortune 500 customers. Pegasus is a highly distributed big data storage and ETL solution that can handle structured, unstructured and semi-structured data within the same architecture using different databases. It is optimized for open source intelligence data and integrates with CodeX's big data platform.
VTrack is a mobile app that allows schools and parents to track student transportation vans. It provides live tracking of each van's location, speed, and route. Parents receive notifications of their child's pick-up and drop-off times. They can also provide feedback to the school. The app aims to ease parents' safety concerns by increasing visibility into their child's transportation. It was originally intended for a university service but shifted focus to grade schools where tracking young kids is most useful.
HearAct is a sign language interpreter for Pakistani Sign Language (PSL) that uses sensors to record hand orientation and gesture coordinates and passes that data to a recognition model to display the corresponding word or sentence. It aims to help the over 250,000 deaf or speech-impaired people in Pakistan communicate by reducing their dependency on others and enabling mobility through a portable, cost-effective solution. The project is supervised by Sir Abdul Basit and developed by team members Ayesha Dojky, Saif Rehman, Shehrbanu Karim, and Zahra Hussaini.
Woxcut is a platform that allows users to create and run cryptocurrency trading bots with custom strategies. It aims to allow users to choose from pre-existing strategies, integrate with existing exchanges via APIs, and run bot instances on the cloud. The platform also seeks to develop an internal machine learning model to help users make optimal trading decisions.
The document describes a project called "Colour It" that aims to automatically colorize grayscale images without human assistance. The system trains a computational neural network on over a million colored images to learn statistical dependencies between image semantics and textures and their colored versions. Users can upload grayscale images to be colorized by the system in a fast and realistic way. The goals are to give users the ability to easily colorize images with minimal processing time and output images that are close to the original ground truths. This technique could benefit medical imaging and colorizing old black and white films while training convolutional neural networks.
GoSpark is a platform that uses beacons and a mobile application to track customer behavior in stores. This allows businesses to gain insights into shopping patterns and trends. The goal is to help retailers increase sales and customer loyalty by providing personalized promotions and a better understanding of customers. The project will require implementing a website and mobile app connected to beacons placed in stores to anonymously track customer movement and send targeted notifications.
1. Beautyou is a virtual makeup applicator that allows users to try on makeup, lenses, and accessories virtually before purchasing through an e-commerce website.
2. The objectives are to build a virtual makeup trier to help users safely apply products virtually and promote online purchases of makeup.
3. Motivations include the growth of the beauty industry, need for solutions to virtually try products at home, and improvements in augmented reality technology.
The document describes a project called "Colour It" that aims to automatically colorize grayscale images without human assistance. The system trains a computational neural network on over a million colored images to learn statistical dependencies between image semantics and textures and their colored versions. Users can upload grayscale images to be colorized by the system in a fast and realistic way. The goals are to give users the ability to easily colorize images with minimal processing time and for the colored image to closely match the original if it was in color. This technique could benefit areas like medical imaging and restoring old black and white films and videos.
The document describes a mobile application called Nan-Baby that connects parents with babysitters. The application was created by students Syeda Ayesha Fahim Junaid Zia Khan Kehkashan Salman and is supervised by Mr. Asad Ali. Nan-Baby aims to provide qualified, educated babysitters to watch children either at the babysitter's home or the parent's home. The motivation was to create opportunities for female students in Pakistan to babysit. The app allows parents to book babysitters near them and choose between having the babysitter come to them or dropping the child off.
Shift is a mobile app that uses image recognition to help online shoppers find products. It allows users to upload photos of items they want to find and it will identify colors, shapes, sizes and product categories to provide matching results. This provides a better search experience than relying only on keywords, as Shift can identify hard-to-describe items. The app aims to reduce average search times for customers and provide a simpler way to find products online through its augmented reality search features.
The document proposes a spatial design solution for social and educational reformation for street children in Karachi. The design includes a master plan with blocks for vocational training, detoxification, rehabilitation and administration, residence, and views. The plan aims to provide street children services for detoxification, rehabilitation, vocational training, residence, and administration.
This document outlines a final year project to develop a scheduling algorithm using genetic algorithms. The project is supervised by Dr. Imran Khan and involves Bushra Qureshi, Maham Faiz, Mariam Imran, and Sheeza Shakeel. The algorithm aims to effectively schedule classes while addressing constraints like classroom availability, professor and student schedules, and course requirements. It will use genetic algorithm operators like initialization, selection, crossover and mutation to generate timetables that satisfy constraints and optimize resource allocation and scheduling. The resulting automated timetable generation process is expected to reduce time spent creating schedules and address issues like clashes in current manual systems.
This document outlines a final year project to design a UAV that can transform into a UGV for 3D mapping and image processing. It includes sections on the overview, block diagram, methodology, flow chart, Gantt chart, and conclusion. The objectives are to create a low-cost hybrid quadcopter that can fly autonomously using sensors and also navigate on the ground for applications like search and rescue, disaster response, and surveillance missions. It proposes using a rolling cage mechanism for the UAV to UGV transformation.
This document discusses using virtual reality exposure therapy with a Kinect motion sensor to treat phobias at medical rehabilitation centers in Pakistan. It proposes developing virtual reality environments that systematically expose patients to phobia triggers, such as heights for acrophobia therapy. Market research found interest from private hospitals to use the tool for treating anxiety disorders. The revenue model would involve subscription or software/hardware packages, and software maintenance costs. Key milestones achieved include designing interfaces for acrophobia therapy with increasing exposure levels and developing early environments for claustrophobia and spider phobia therapy.
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1. Department of Electrical Engineering,
University of Engineering and Technology, Lahore
Protein Quantitation Pipeline For Top Down
Proteomics
(Hudiara Drain Case Study)
Group No: 2014-FYP-14
Project Advisor: Dr. Khalid Mahmood Ul Hasan
Undergraduate Final Year Project Presentation
Dated: 4th April, 2018
2. Team Introduction
Muhammad Ahsan Ali (Team Leader)
2014-EE-024
Specialization: Computer
Undergraduate Final Year Project Presentation
Dated: 4th April, 2018
Rimsha Nadeem
2014-EE-057
Specialization: Computer
Mujtaba Saboor
2014-EE-016
Specialization: Computer
Shifa Imran
2014-EE-158
Specialization: Computer
3. Problem Statement
• Lack of open-source and open-architecture softwares
publicly available for the analysis of mass
spectrometric data employing top-down approach.
• Limited research work on protein quantitation through
top-down proteomics.
Undergraduate Final Year Project Presentation
Dated: 4th April, 2018
4. Problem Statement
• Extremely dangerous heavy metal poisoning in Hudiara
drain, Lahore.
• Heavy metal poisoned water used for drinking purposes
and feeding crops causing serious health effects on
general public.
Undergraduate Final Year Project Presentation
Dated: 4th April, 2018
5. Problem Statement
• Pollution Load Contributed by Hudiara drain to River
Ravi: 141.5 tons/day[2]
• Its annual average discharge at its confluence with the
river Ravi is 178 cusecs[3]
• Process of bioremediation at stake due to the addition
of antibiotics, in the polluted Hudiara drain, originating
from industrial effluents from both India and Pakistan
Undergraduate Final Year Project Presentation
Dated: 4th April, 2018
6. Heavy Metals Reported In Hudiara Drain
Undergraduate Final Year Project Presentation
Dated: 4th April, 2018
Effects of Metals on Human Health:
• Cr: Damage to liver, kidneys, nerve tissues,
cancers and skin irritation.
• Mn: Manganese, tremors, and increased
neurological disorders in children,
hyperactivity, memory issues.
• Fe: Acne, Eczema, Hemochromatosis,
which can lead to liver, heart and pancreatic
damage, as well as diabetes.
• Cu: Short-term exposure to high levels can
cause gastrointestinal distress. Long-term
exposure and severe cases of copper
poisoning can cause anaemia and disrupt
liver and kidney functions.
• Cd: Kidney Dysfunction and Osteoporosis.
• Pb: Young children, infants, and foetuses
are particularly vulnerable
• As: Skin, bladder and lung cancers, skin
lesions, cardiovascular disease,
neurotoxicity and diabetes.
7. Problem Statement: Hudiara Drain
Undergraduate Final Year Project Presentation
Dated: 4th April, 2018
Snapshot of Case Study of Hudiara. Pinned locations show Industries, Blue Line is Hudiara Drain, Black Line is
Sattukatla Drain, Arrows Starred sites are sampling sites, Yellow region is residential area and green region is
Quaid-e-Azam Industrial Estate.
8. Proposed Solution: Hudiara Case Study
Bioremediation is the use of microbes to clean up
contaminated soil and groundwater.
Undergraduate Final Year Project Presentation
Dated: 4th April, 2018
1Biosorption: Binding
of metals to cellular
surface.
2Bioaccumulation:
Active uptake and
accumulation in
cytoplasm/periplasm
ic space.
3Biopreciptation: Metal ions
combine with the anionic
species excreted by microbial
metabolism to give less toxic,
insoluble, metal salts.
4Biotransformation:
Chemical modification of a
toxic compound to less toxic
compound.
5Bioleaching: Conversion
of insoluble metal sulfides
to soluble metal sulfates.
9. Proposed Solution : Hudiara Case Study
• Perform analysis of the protein content of the microbes
present in Hudiara drain responsible for heavy metal
fixation, which can lead to unlock plethora of ways to
unfold the problem of heavy metal contamination in
Pakistan and all around the world.
• Identify proteins responsible for each heavy metal
fixation, and quantify the amount necessary for
substantial bioremediation in order for the water to be
non-injurious to human health.
Undergraduate Final Year Project Presentation
Dated: 4th April, 2018
10. Proposed Solution
• Develop a state-of-the-art high-performance protein
MS/MS mass spectra deconvolution, theoretical pattern
generation, protein identification and quantitation
pipeline for this purpose.
• Utilize groundbreaking Graphical Processing Units
(GPUs) for implementing intensive algorithms.
• Implement entire workflow as a RESTful API Web-
Service , with its core built on C#, front-end developed
using Angular 4 (a JavaScript framework), with an
MSSQL database present at its back-end.
Undergraduate Final Year Project Presentation
Dated: 4th April, 2018
11. Ultimate Goal
• Opening a new paradigm of research by finding specific
proteins responsible for each heavy metal fixation.
• Using our results, help bioengineer novel ways to combat the
issue of heavy metal contamination employing the technique
of bioremediation.
• Make the entire pipeline open-source and open-architecture
for general public for future developments.
• Move on to protein analysis in milk, blood and other
substances for further expansion.
Undergraduate Final Year Project Presentation
Dated: 4th April, 2018
14. Web Architecture
• Algorithmic codes are written in
C# and specific hot-paths shifted
to GPU through CUDA C coding
(host approach kernel and ).
• All input parameters, results and
other essentials are stored in
database through code first
technique.
• RESTful API is connected to
Angular 4 front-end.
Undergraduate Final Year Project Presentation
Dated: 4th April, 2018
16. GPU Introduction
• CPU is the central processing unit and is considered as the brain of the
computing devices. CPU is a general purpose it can do any
computation and can process various tasks while GPU is a specialized
unit that can do some specific tasks more efficiently.
• GPU has hundreds of cores that can handle thousands of threads at a
time thus is useful for large bulk of data, while a CPU can handle only
few threads of software at a time. The cost of a CPU thread switch is
hundreds of cycles whereas GPU does not have any cost in switching
of threads.
• Since our input files contain plethora of mass-intensity pair values, it’s
much more efficient it to implement our algorithms using GPUs.
Undergraduate Final Year Project Presentation
Dated: 4th April, 2018
18. Algorithms
State-of-the-art algorithms have been designed under
these categories:
I. Theoretical Pattern Generation using Averagine[4].
II. Deconvolution of protein spectra using a modified
version of THRASH[5].
III. Extraction of missing peaks using Polynomial
Regression.
IV.Protein Quantitation using Spectral Counting[6].
V. Protein Quantitation using XIC[7].
Undergraduate Final Year Project Presentation
Dated: 4th April, 2018
19. I. Theoretical Pattern Generator
• Multinomial Expansion is used to find out the intensities for a
specific number of atoms and is described below:
(𝑝 + 𝑞) 𝑛 = 𝑥=0
𝑛
𝐶(𝑛, 𝑥) 𝑝(𝑛−𝑥) 𝑞 𝑥 Eq(1)
where 𝐶 𝑛, 𝑥 =
𝑛!
𝑛−𝑥 ! 𝑥!
,
𝑝 = abundance of lighter isotope,
q = abundance of heavier isotope,
n = number of atoms
Undergraduate Final Year Project Presentation
Dated: 4th April, 2018
20. Undergraduate Final Year Project Presentation
Dated: 4th April, 2018
• For large molecules, the result of the factorial becomes very taxing, it is
optimized by a log operator and Sterling's approximation. Taking log of
equation 1:
𝑙𝑜𝑔
𝑛!
𝑛−𝑥 ! 𝑥!
× 𝑝 𝑥 × 𝑞 𝑛−𝑥 =
𝑙𝑜𝑔 𝑛! + [𝑥 × 𝑙𝑜𝑔 𝑝 ] + [ 𝑛 − 𝑥 × 𝑙𝑜𝑔 𝑞 ] − 𝑙𝑜𝑔 𝑥! − 𝑙𝑜𝑔 𝑛 − 𝑥 !
𝑤ℎ𝑒𝑟𝑒: 𝑙𝑜𝑔 𝑛! = 𝑛 × 𝑙𝑜𝑔 𝑛 − 𝑛 + 𝑙𝑜𝑔(𝑛)
• Anti-log of the above calculation gives us the required theoretical
intensity for that particular instance.
21. II. Deconvolution
Undergraduate Final Year Project Presentation
Dated: 4th April, 2018
Get .RAW file,
Extract mass list and
intensities
End of mass/
intensity list?
End
Find local maxima
within a user defined
window
Get molecular
formula from
Averagine and
generate theoretical
spectrum
Identify peak spacing
(z)
Find Goodness of Fit
between
experimental and
theoretical
1/z an ineger?
p value less than
threshold?
Subtract 1.0023 from
the average mass
Process original
spectrum
Create mass list of
mono isotopic masses
START
YES
NO
NO
YES
YESNO
22. Comparison With a Chinese Toolbox
• Results of our In-house
deconvolution tool
• Results of a Chinese research
group
Undergraduate Final Year Project Presentation
Dated: 4th April, 2018
C100 H200 O60 N50 S3
MASS INTENSITY
3156 75.7747
3157 100.0000
3158 74.9352
3159 40.8380
3160 17.8889
3162 6.6406
3163 2.1641
3164 0.6284
3165 0.1665
24. Applications
• Identification and quantitation of proteins is of critical
importance in pharmaceutical industries.
• Diagnosis of diseases due to malfunctioning of a
protein.
• Other than water pollution, many other case studies can
be presented as identification of a protein specific to a
function can open vast horizons of research, like
hemoglobin for oxygen fixation in cells.
• Analysis of the protein content of milk, thus
determining milk quality. Undergraduate Final Year Project Presentation
Dated: 4th April, 2018
25. Audience
• All kinds of computer engineers, biologists, chemists,
doctors, pharmacists and bioengineers who work in any
kind of lab and want to test their results with the help of
mass spectrometry.
Undergraduate Final Year Project Presentation
Dated: 4th April, 2018
26. What we have done so far?:
• All the designed algorithms are verified and
benchmarked on MATLAB.
• A MATLAB version of our toolbox is already available at
GITHUB.
• Web service is live at: 203.135.63.99/perceptron_v1
• Hudiara samples have been collected from six different
sites and sent for mass spectrometry after proper wet lab
procedure, raw data files are awaited.
Undergraduate Final Year Project Presentation
Dated: 4th April, 2018
27. What we have done so far?:
• Mass Tuner, PST and Spectral Counting are
implemented on GPU for higher performance.
Undergraduate Final Year Project Presentation
Dated; 4th April, 2018
28. GUI Developed
• Perceptron: A RESTful API Web-Service (GPU-based)
• The front-end developed using Angular 4 (a JavaScript framework).
• Core built using C#
• MSSQL database present at the back end.
Undergraduate Final Year Project Presentation
Dated: 4th April, 2018
29. GUI Developed
• Spectrum: A MATLAB toolbox
Undergraduate Final Year Project Presentation
Dated: 4th April, 2018
30. Future Deliverables
• Incorporate quantitation of labelled data samples e.g.
SILAC, iTRAQ, iCAT etc.
• Interface multiple GPUs to prevent stallation in queued
jobs and further boost the computational processes.
• Help innovate new ways to combat the issue of water
contamination employing bioengineering.
Undergraduate Final Year Project Presentation
Dated: 4th April, 2018
31. Gantt Chart
Undergraduate Final Year Project Presentation
Dated: 4th April, 2018
0 10 20 30 40 50 60 70
Deconvolution
Quantitation
Spectrum
Perceptron
Milestones Achieved from 15 Feb 17’ to 1 April 18’ (58 weeks)
GUI/frontend GPU tansfer Algorithms design
32. References
Undergraduate Final Year Project Presentation
Dated: 4th April, 2018
[1] Environ. D. Valkenborg I. Jansen, and T. Burzykowski
“A Model-Based Method for the Prediction of the Iso-Mental
Monitoring of River Ravi,” in EPA, pp. 1-86, 2009.
[2] M. T. Yamin, N. Ahmad, (2007). “Influence of Hudiara Drain
Water Irrigation on Trace Elements Load in Soil and Uptake by
Vegetables,” Journal of Applied Sciences and Environmental
Management [Online], vol. 11, no. 2, pp. 169-172.
https://doi.org/10.4314/jasem.v11i2.55029
33. References
Undergraduate Final Year Project Presentation
Dated: 4th April, 2018
[3] M. S. Nobile, “cuTauLeaping: A GPU-Powered Tau-Leaping
Stochastic Simulator for Massive Parallel Analyses of Biological
Systems”, in PLOS ONE, 2014.
[4] D. Valkenborg, I. Jansen, T. Burzykowski, “A Model-Based
Method for the Prediction of the Isotopic Distribution of
Peptides”, in Journal of American Society for Mass Spectrometry,
2008.
34. References
Undergraduate Final Year Project Presentation
Dated: 4th April, 2018
[5] D. M. Horn, “Automated reduction and interpretation of high
resolution electrospray mass spectra of large molecules”, in Journal
of American Society for Mass Spectrometry, 2000.
[6] K. Aoshima, “A Simple Peak Detection and Label Free
Quantitation Algorithm for Chromatography Mass Spectrometry”,
in BMC, 2014.
[7] D. Fermin, “Abacus: A computational Tool for Extracting and
Pre-processing Spectral Count Data” in Proteomics, vol. 11, no. 7,
2011.