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Item Accelerating complex modeling workflows in CyberWater using on-demand HPC/Cloud resources(IEEE, 2021-09) Li, Feng; Chen, Ranran; Fu, Yuankun; Song, Fengguang; Liang, Yao; Ranawaka, Isuru; Pamidighantam, Sudhakar; Luna, Daniel; Liang, Xu; Computer Information and Graphics Technology, School of Engineering and TechnologyWorkflow management systems (WMSs) are commonly used to organize/automate sequences of tasks as workflows to accelerate scientific discoveries. During complex workflow modeling, a local interactive workflow environment is desirable, as users usually rely on their rich, local environments for fast prototyping and refinements before they consider using more powerful computing resources. However, existing WMSs do not simultaneously support local interactive workflow environments and HPC resources. In this paper, we present an on-demand access mechanism to remote HPC resources from desktop/laptop-based workflow management software to compose, monitor and analyze scientific workflows in the CyberWater project. Cyber-Water is an open-data and open-modeling software framework for environmental and water communities. In this work, we extend the open-model, open-data design of CyberWater with on-demand HPC accessing capacity. In particular, we design and implement the LaunchAgent library, which can be integrated into the local desktop environment to allow on-demand usage of remote resources for hydrology-related workflows. LaunchAgent manages authentication to remote resources, prepares the computationally-intensive or data-intensive tasks as batch jobs, submits jobs to remote resources, and monitors the quality of services for the users. LaunchAgent interacts seamlessly with other existing components in CyberWater, which is now able to provide advantages of both feature-rich desktop software experience and increased computation power through on-demand HPC/Cloud usage. In our evaluations, we demonstrate how a hydrology workflow that consists of both local and remote tasks can be constructed and show that the added on-demand HPC/Cloud usage helps speeding up hydrology workflows while allowing intuitive workflow configurations and execution using a desktop graphical user interface.Item Access to Knowledge in Brazil: New Research on Intellectual Property, Innovation and Development(Bloomsbury Academic, 2010) Shaver, LeaAccess to knowledge is a demand for democratic participation, for global inclusion and for economic justice. It is a reaction to the excessively restrictive international IP regime put in place over the last two decades, which seeks to reassert the public interest in a more balanced information policy. With sponsorship from the Ford Foundation, the Information Society Project at Yale Law School has embarked on a new series of access to knowledge research, in partnership with colleagues in Brazil, China, Egypt, Ethiopia, India, Russia and South Africa. The first book in this series, Access to Knowledge in Brazil, focuses on current issues in intellectual property, innovation and development policy from a Brazilian perspective. Each chapter is authored by scholars from the Fundação Getulio Vargas law schools in São Paolo and Rio de Janeiro and examines a policy area that significantly impacts access to knowledge in the country. These include: exceptions and limitations to copyright, free software and open business models, patent reform and access to medicines, and open innovation in the biotechnology sector.Item Access to Knowledge in Egypt: New Research on Intellectual Property, Innovation and Development(Bloomsbury Academic, 2010) Shaver, Lea; Rizk, NaglaThe conventional wisdom in Egypt examines the issue of intellectual property solely as a question of policing and enforcement. The high levels of protection indicated by the WTO Agreement on Trade Related Aspects of Intellectual Property Rights are unquestioningly assumed to be desirable. Policy debates - and all too often academic ones as well - focus only on the questions of how to more efficiently tighten IP protection and crack down on piracy. Yet a more critical examination is urgently needed, whereby IP law, policy, and practice are viewed from a development perspective, rather than from an enforcement perspective. This volume takes on this endeavor. It offers the first examination of IP issues in Egypt adopting a multidisciplinary bottom-up approach that aims at maximizing access and contribution to knowledge, and in turn, promoting development. Bringing rigorous empirical research to bear on unquestioned ideologies, the collaborating authors question the conventional wisdom that more IP protection is necessarily better for innovation and development.Item An Open Source Platform for Computational Histopathology(IEEE, 2021) Yu, Xiaxia; Zhao, Bingshuai; Huang, Haofan; Tian, Mu; Zhang, Sai; Song, Hongping; Li, Zengshan; Huang, Kun; Gao, Yi; Biostatistics and Health Data Science, School of MedicineComputational histopathology is a fast emerging field which converts the traditional glass slide based department to a new examination platform. Such a paradigm shift also brings the in silico computation to the field. Much research have been presented in the past decades on the algorithm development for pathology image analysis. On the other hand, a comprehensive software platform with advanced visualization and computation capability, large developer community, flexible plugin mechanism, and friendly transnational license, would be extremely beneficial for the entire community. In this work, we present SlicerScope: an open platform for whole slide histopathology image computing based on the highly successful 3D Slicer. We present rationale on the choice of such an architecture, introducing new modules/tools for giga-pixel whole slide image viewing, and four specific analytical modules for qualitative presentation, nucleus level analysis, tissue scale computation, and 3D pathology. The entire software is publicly available at https://slicerscope.github.io/ , facilitating the algorithmic, clinical, and transnational researches.Item AutoCCS: automated collision cross-section calculation software for ion mobility spectrometry-mass spectrometry(Oxford University Press, 2021) Lee, Joon-Yong; Bilbao, Aivett; Conant, Christopher R.; Bloodsworth, Kent J.; Orton, Daniel J.; Zhou, Mowei; Wilson, Jesse W.; Zheng, Xueyun; Webb, Ian K.; Li, Ailin; Hixson, Kim K.; Fjeldsted, John C.; Ibrahim, Yehia M.; Payne, Samuel H.; Jansson, Christer; Smith, Richard D.; Metz, Thomas O.; Chemistry and Chemical Biology, School of ScienceMotivation: Ion mobility spectrometry (IMS) separations are increasingly used in conjunction with mass spectrometry (MS) for separation and characterization of ionized molecular species. Information obtained from IMS measurements includes the ion's collision cross section (CCS), which reflects its size and structure and constitutes a descriptor for distinguishing similar species in mixtures that cannot be separated using conventional approaches. Incorporating CCS into MS-based workflows can improve the specificity and confidence of molecular identification. At present, there is no automated, open-source pipeline for determining CCS of analyte ions in both targeted and untargeted fashion, and intensive user-assisted processing with vendor software and manual evaluation is often required. Results: We present AutoCCS, an open-source software to rapidly determine CCS values from IMS-MS measurements. We conducted various IMS experiments in different formats to demonstrate the flexibility of AutoCCS for automated CCS calculation: (i) stepped-field methods for drift tube-based IMS (DTIMS), (ii) single-field methods for DTIMS (supporting two calibration methods: a standard and a new enhanced method) and (iii) linear calibration for Bruker timsTOF and non-linear calibration methods for traveling wave based-IMS in Waters Synapt and Structures for Lossless Ion Manipulations. We demonstrated that AutoCCS offers an accurate and reproducible determination of CCS for both standard and unknown analyte ions in various IMS-MS platforms, IMS-field methods, ionization modes and collision gases, without requiring manual processing. Availability and implementation: https://github.com/PNNL-Comp-Mass-Spec/AutoCCS. Supplementary information: Supplementary data are available at Bioinformatics online. Demo datasets are publicly available at MassIVE (Dataset ID: MSV000085979).Item CentFlow: Centrality-Based Flow Balancing and Traffic Distribution for Higher Network Utilization(IEEE, 2017) Challa, R.; Jeon, S.; Kim, D. S.; Choo, H.; Electrical and Computer Engineering, School of Engineering and TechnologyNext-generation networks (NGNs) are embracing two key principles of software defined networking (SDN) paradigm functional segregation of control and forwarding plane, and logical centralization of the control plane. A centralized control enhances the network management significantly by regulating the traffic distribution dynamically and effectively. An eagle-eye view of the entire topology opens up the opportunity for an SDN controller to refine the routing. Optimizing the network utilization in terms of throughput is majorly dependent on the routing decisions. Open Shortest Path First (OSPF) and Intermediate System to Intermediate System (IS-IS) are well-known traditional link state routing protocols proven with operation over operator networks for a long time. However, these classical protocols deployed distributively fall short of expectation in addressing the current routing issues due to the lack of a holistic view of the network topology and situation, whereas handling enormous traffic and user quality of experience (QoE) requirements are getting critical. IP routing in NGN is widely expected to be supported by SDN to enhance the network utilization in terms of throughput. We propose a novel routing algorithm-CentFlow, for an SDN domain to boost up the network utilization. The proposed weight functions in CentFlow achieve smart traffic distribution by detecting highly utilized nodes depending on the centrality measures and the temporal node degree that changes based on node utilization. Furthermore, the frequently selected edges are penalized thereby augmenting the flow balancing and dispersion. CentFlow reaps greater benefits on an SDN controller than the classical OSPF due to its comprehensive view of the network. Experimental results show that CentFlow enhances the utilization of up to 62% of nodes and 49% of links, respectively, compared to an existing Dijkstra algorithm-based routing scheme in SDN. Furthermore, nearly 6.5% more flows are processed networ- wide.Item Cypiripi: exact genotyping of CYP2D6 using high-throughput sequencing data(Oxford University Press, 2015-06-15) Numanagic, Ibrahim; Malikic, Salem; Pratt, Victoria M.; Skaar, Todd C.; Flockhart, David A.; Sahinalp, S. Cenk; Department of Medicine, IU School of MedicineMOTIVATION: CYP2D6 is highly polymorphic gene which encodes the (CYP2D6) enzyme, involved in the metabolism of 20-25% of all clinically prescribed drugs and other xenobiotics in the human body. CYP2D6 genotyping is recommended prior to treatment decisions involving one or more of the numerous drugs sensitive to CYP2D6 allelic composition. In this context, high-throughput sequencing (HTS) technologies provide a promising time-efficient and cost-effective alternative to currently used genotyping techniques. To achieve accurate interpretation of HTS data, however, one needs to overcome several obstacles such as high sequence similarity and genetic recombinations between CYP2D6 and evolutionarily related pseudogenes CYP2D7 and CYP2D8, high copy number variation among individuals and short read lengths generated by HTS technologies. RESULTS: In this work, we present the first algorithm to computationally infer CYP2D6 genotype at basepair resolution from HTS data. Our algorithm is able to resolve complex genotypes, including alleles that are the products of duplication, deletion and fusion events involving CYP2D6 and its evolutionarily related cousin CYP2D7. Through extensive experiments using simulated and real datasets, we show that our algorithm accurately solves this important problem with potential clinical implications.Item Identification of ultramodified proteins using top-down tandem mass spectra(American Chemical Society, 2013-12-06) Liu, Xiaowen; Hengel, Shawna; Wu, Si; Tolić, Nikola; Pasa-Tolić, Ljiljana; Pevzner, Pavel A.; Department of BioHealth Informatics, IU School of Informatics and ComputingPost-translational modifications (PTMs) play an important role in various biological processes through changing protein structure and function. Some ultramodified proteins (like histones) have multiple PTMs forming PTM patterns that define the functionality of a protein. While bottom-up mass spectrometry (MS) has been successful in identifying individual PTMs within short peptides, it is unable to identify PTM patterns spreading along entire proteins in a coordinated fashion. In contrast, top-down MS analyzes intact proteins and reveals PTM patterns along the entire proteins. However, while recent advances in instrumentation have made top-down MS accessible to many laboratories, most computational tools for top-down MS focus on proteins with few PTMs and are unable to identify complex PTM patterns. We propose a new algorithm, MS-Align-E, that identifies both expected and unexpected PTMs in ultramodified proteins. We demonstrate that MS-Align-E identifies many proteoforms of histone H4 and benchmark it against the currently accepted software tools.Item Improving a library workshop service: Implementing change and enhancing the service based on data analysis(Emerald Insight, 2023-08-29) Stumpff, Julia C.; Craven, Hannah J.PURPOSE This paper aims to describe how one medical library implemented a new scheduling system, initiated data analysis and modified its regularly scheduled workshop program because of evidence-based decision-making. Academic libraries that struggle with workshop attendance may use this process as a model. DESIGN/METHODOLOGY/APPROACH Workshop registration data analysis focused on registrants' affiliation, role and location, and how registrants learned of workshops. Workshop attendance data analysis focused on which workshops, days, times of the day and months had the highest attendance. The analysis led to changes in marketing and targeted scheduling of future workshops by the time of day, day of the week and month of the year. FINDINGS Data collected for four years, fall 2018 – summer 2022 (12 semesters), shows a steady increase in the number of people attending library workshops. The increase in attendance and ROI experienced after the changes implemented at Ruth Lilly Medical Library (RLML) is significant as libraries often struggle with attendance, marketing and return on investment when offering ongoing educational workshops. ORIGINALITY/VALUE Many libraries offer ongoing workshops with low attendance. This article provides an example of how one library changed software and registration and implemented evidence-based decision-making related to scheduling which may have contributed to an increase in workshop attendance. Other academic libraries might consider adopting similar software and evidence-based decision-making to improve their library workshop service.Item Large-scale open-source three-dimensional growth curves for clinical facial assessment and objective description of facial dysmorphism(Springer Nature, 2021-06-09) Matthews, Harold S.; Palmer, Richard L.; Baynam, Gareth S.; Quarrell, Oliver W.; Klein, Ophir D.; Spritz, Richard A.; Hennekam, Raoul C.; Walsh, Susan; Shriver, Mark; Weinberg, Seth M.; Hallgrimsson, Benedikt; Hammond, Peter; Penington, Anthony J.; Peeters, Hilde; Claes, Peter D.; Biology, School of ScienceCraniofacial dysmorphism is associated with thousands of genetic and environmental disorders. Delineation of salient facial characteristics can guide clinicians towards a correct clinical diagnosis and understanding the pathogenesis of the disorder. Abnormal facial shape might require craniofacial surgical intervention, with the restoration of normal shape an important surgical outcome. Facial anthropometric growth curves or standards of single inter-landmark measurements have traditionally supported assessments of normal and abnormal facial shape, for both clinical and research applications. However, these fail to capture the full complexity of facial shape. With the increasing availability of 3D photographs, methods of assessment that take advantage of the rich information contained in such images are needed. In this article we derive and present open-source three-dimensional (3D) growth curves of the human face. These are sequences of age and sex-specific expected 3D facial shapes and statistical models of the variation around the expected shape, derived from 5443 3D images. We demonstrate the use of these growth curves for assessing patients and show that they identify normal and abnormal facial morphology independent from age-specific facial features. 3D growth curves can facilitate use of state-of-the-art 3D facial shape assessment by the broader clinical and biomedical research community. This advance in phenotype description will support clinical diagnosis and the understanding of disease pathogenesis including genotype–phenotype relations.
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