208 research outputs found
DOE Climate Change Research Program: Strategic Plan
Advance the forefront of climate change research to provide the nation with the scientific knowledge it needs about the effects of greenhouse gas emissions on Earth\u27s climate and biosphere to support effective energy and environmental decision making
New and improved proteomics technologies for understanding complex biological systems: Addressing a grand challenge in the life sciences
Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/93688/1/pmic7183.pd
Report on the Third Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE3)
This report records and discusses the Third Workshop on Sustainable Software
for Science: Practice and Experiences (WSSSPE3). The report includes a
description of the keynote presentation of the workshop, which served as an
overview of sustainable scientific software. It also summarizes a set of
lightning talks in which speakers highlighted to-the-point lessons and
challenges pertaining to sustaining scientific software. The final and main
contribution of the report is a summary of the discussions, future steps, and
future organization for a set of self-organized working groups on topics
including developing pathways to funding scientific software; constructing
useful common metrics for crediting software stakeholders; identifying
principles for sustainable software engineering design; reaching out to
research software organizations around the world; and building communities for
software sustainability. For each group, we include a point of contact and a
landing page that can be used by those who want to join that group's future
activities. The main challenge left by the workshop is to see if the groups
will execute these activities that they have scheduled, and how the WSSSPE
community can encourage this to happen
Bioinformatics
This book is divided into different research areas relevant in Bioinformatics such as biological networks, next generation sequencing, high performance computing, molecular modeling, structural bioinformatics, molecular modeling and intelligent data analysis. Each book section introduces the basic concepts and then explains its application to problems of great relevance, so both novice and expert readers can benefit from the information and research works presented here
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An Informatics Roadmap Toward a FAIR Understanding of Mitochondrial Biology and Rare Mitochondrial Disease
Mitochondrial biology is integral to our fundamental understanding of human health and many diseases. They exist in every human cell type except for red blood cells and have critical functions in metabolism, oxidative phosphorylation, oxidation-reduction, and as signaling hubs responsible for mediating protective mechanisms. Rare mitochondrial diseases (RMDs) are devastating and complex, affect multiple organ systems, and disproportionately impact young children. Despite copious existing knowledge and increased public interest, the knowledge is fragmented and difficult to access. Clinical case reports (CCRs) on RMDs contain valuable clinical insights, but they are scarce and lack the metadata necessary to facilitate their discovery among the two million CCRs on PubMed. The unstructured text data of CCRs is also ill-suited to computational approaches, limiting our ability to derive the knowledge contained within.To address these issues, I assembled all available informatics tools and resources with mitochondrial components and used them to contribute to Gene Wiki pages that enable easy access to mitochondrial knowledge for researchers, students, clinicians, and patients. Through these efforts, I made mitochondrial gene, protein, and disease knowledge widely accessible with contributions of over 4MB of content across 541 Gene Wiki pages. Concurrently, I used Gene Wiki as an educational platform to train over 50 students in the biosciences and pre-medical studies in mitochondrial biology and disease, as well as instilling effective research and writing methods in biomedicine.To impose structure on CCRs and render them FAIR (Findable, Accessible, Interoperable, Reusable), I developed and applied a standardized metadata template to RMD CCRs and codified patient symptomology with the International Statistical Classification of Disease and Related Health Problems (ICD) system. I created the open-source, cloud-based MitoCases RMD Knowledge Platform (http://mitocases.org/) to house data on 384 RMD CCRs, including 4,561 instances of 952 unique ICD codes. Supplementing CCRs with structured metadata amplifies machine-readable information content and provides a distinct improvement in searching for CCRs as compared to indexing by title and abstract. Finally, I employed these resources to conduct a thorough review of Barth syndrome and characterized the diversity of presentations, range of genetic etiologies, and treatment paradigms
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