OSFair2017 Workshop | West-Life: world-wide e-infrastructure for structural biology

•

0 likes•286 views

Chris Morris presents West-Life, a world-wide e-infrastructure for structural biology | OSFair2017 Workshop Workshop title: Open Science as a service: tools for research communities Workshop overview: The aim of this workshop is to work with research communities especially interested/relevant to open science publishing paradigms: publishing of literature, datasets, methods, and experiments for reproducibility and transparent assessment of science. This will be an interactive session with communities presenting their requirements and current tooling to identify overlaps, better and cost-effective solutions. When: DAY 2 - PARALLEL SESSION 3

West-Life:
World-wide E-infrastructure for
structural biology
Chris Morris, STFC

Outlook
• Structural biology aims to understand the molecular
basis of life
• Experimental centres
– Synchrotrons (MX), 47 in world
– Electron microscopes (EM), rapid growth
– Nuclear Magnetic Resonance (NMR) instruments, ~200 in Europe
– A long tail of other techniques
• Researchers in every university
– And in pharmaceutical companies
– Around 25,000 structural experiments per year

Scientific Process
• Identify a protein of interest (“target”)
• Make recombinant DNA (“construct”)
• Express in E.Coli or other tractable culture
• Purify
• Can crystallize? MX
• Can’t crystallize? EM, NMR etc
• Determine structure using software tools
– Automatic for simpler MX structures
– Months of guided computation for some EM structures
• Publish…
Sample
Prep.

Scholarly communication practices
• Literature
– Life Sciences papers are often open
access
• Datasets:
– Final structure is deposited in Protein
Data Bank
– Intermediate data too
• Software suites and services
– CCP4, Phenix, weNMR
– Rapid developments for EM
PDB new entries / year
(log scale)

Scholarly communication desiderata
• Archiving experimental data
– Some progress, but 100M for MX, 1TB for EM
– XFEL a firehose
– full access for reviewers
• Full provenance, structure to sample
– Reproducibility of sample prep is poor
• Reproducibility of processing
– PDB-REDO reprocesses with latest algorithms
• Automatic acquisition of metadata
– Scientists don’t like housekeeping

For more detail…
The Life Cycle of Structural Biology Data
https://www.rd-alliance.org/group/structural-biology-
ig/outcomes/life-cycle-structural-biology-data
Corresponding author: Chris Morris
Contributors: Claudia Alen, Lucia Banci, Alexandre Bonvin, Pablo Conesa, Alfonso
Duarte, John Helliwell, Rob Hooft, Brian Matthews, Antonio Rosato, Sameer Velankar,
Geerten Vuister, John Westbrook, Martyn Winn

FAIRPORT is an international project to develop a lightweight interoperability architecture for biomedical - and potentially other - data repositories. This slide deck is a presentation to the FAIRPORT technical team. It describes a proposed model for supporting domain-specific search metadata using a common schema model across all repositories. The proposal makes use of the following existing technologies, with minor extensions: - the W3C DCAT model for dataset description - the W3C SKOS knowledge organization system - OWL2 Ontology Language - Dublin Core Vocabulary - NCBO Bioportal biomedical ontologies collection

NgspTim Clark

Ontology-Based Word Sense Disambiguation for Scientific LiteratureeXascale Infolab

User experience of Encore: a mental models approach

Andrew Preater

OSFair2017 Workshop | Big Mechanism: deep reading for cancer biology

Open Science Fair

Sophia Ananiadou talks about big mechanisms (from text to experiments using their text mining) Training title:TDM unlocking a goldmine of information Training overview: Text and Data Mining (TDM) is a natural ‘next step’ in open science. It can lead to new and unexpected discoveries and increase the impact of publications and repositories. This workshop showcases examples of successful TDM and infrastructural solutions for researchers. We will also discuss what is needed to make most of infrastructures and how publishers and repositories can open up their content. DAY 2 - PARALLEL SESSION 4 & 5

evolutionary game theory presentation

Yiming Yu, Msc, ARe, CEEM,CFA Level I passed

The core content discusses the terminology used in Systems Sciences, the systems thinking/approach or Systemics. Focus is kept on Systems Biology for the most part of the presentations where it is compared with other disciplines and examples of Systems Biology approach and challenges of systems science are also discussed. The sad thing about uploading this to Slide Share is that animations don't work.

Bioinformatics__Lecture_1.ppt

sirwansleman

Ewan Birney Biocuration 2013

Iddo

How do we know what we don’t know: Using the Neuroscience Information Framew...

Maryann Martone

Mauricio carrillo trippguadalupe.moreno

2014 09 30_t1_bioinformatics_wim_vancriekinge

Prof. Wim Van Criekinge

Computer science history.pdf

sirwansleman

Recently, it was reported that the forkhead box O (FoxO) transcription factor promotes human cytomegalovirus (HCMV) replication via direct binding to the promoters of the major immediate-early (MIE) genes, but how the FoxO factor impacts HCMV replication remains unknown. In this report, we found that human cytomegalovirus (HCMV), a beta herpesvirus member, could dramatically induce the expression of FOXOs in the infected human fibroblasts. The induced FOXOs were recruited into the viral replication compartments (vRC) in the nucleus, especially at the late stage of infection. Suppression of FOXO expression by RNA interference significantly inhibited HCMV replication, and the production of progeny virus was reduced remarkably. Mechanistically, FOXO knockdown intensively crippled viral late gene expression at the transcriptional level, while it only marginally affected viral DNA synthesis. This study highlights how FoxO enhances HCMV gene transcription and viral replication to promote productive infection

RDAP14: Maryann Martone, Keynote, The Neuroscience Information Framework

ASIS&T

Overview of cheminformatics

Benjamin Bucior

Biological databases

SEKHARREDDYAMBATI

Neuroscience as networked science

Neuroscience Information Framework

Biological Database (1)pptxpdfpdfpdf.pdf

BioinformaticsCentre

485 lec3 history_review_ii

hhalhaddad

A knowledge capture framework for domain specific search systems

ramakanz

Introduction to Bioinformatics

jaumebp

Clustering the royal society of chemistry chemical repository to enable enhan...

Valery Tkachenko

The Royal Society of Chemistry has hosted the ChemSpider database and associated platforms for over five years. Technologies made significant progress over that period but, more importantly, the community needs in terms of the variety of data types as well as search performance have increased. The preprocessing of chemicals for improved similarity searching and compound database navigation is seen as one crucial component of major development efforts to architect a new data repository. This component is engineered and implemented in collaboration with the group of Professor Oliver Kohlbacher at University of Tübingen. They have developed an approach for clustering large chemical libraries based on a fast, parallel, and purely CPU-based algorithm for 2D binary fingerprint similarity calculation. Using this method, the complete similarity network of our seed set with tens of millions of chemicals has been analyzed at a Tanimoto threshold of 0.6 and all similarity links were fed into our database. The latter is highly beneficial and will allow us to create more complex and enriching visualizations of similar compounds with associated bioactivity data and physicochemical properties for the RSC chemical repository users. This presentation will provide an overview of our experiences in applying clustering to our compound data and how it will be used to enrich data navigation on the RSC data repository.

2015 bioinformatics wim_vancriekinge

Prof. Wim Van Criekinge

OSFair2017 workshop | Monitoring open science trends in europe

Open Science Fair

Salil Gunashekar presents topen science trends in europe Workshop title: Open Science Monitor Workshop overview: Which are the measurable components of Open Science? How do we build a trustworthy, global open science monitor? This workshop will discuss a potential framework to measure Open Science, including the path from the publishing of an open policy (registries of policies and how these are represented or machine read), to the use of open methodologies, and the opening up of research results, their recording and measurement. DAY 2 - PARALLEL SESSION 5

OSFair2017 Worksop | NUCLEUS project - Are you ready to perform in RRI ecosys...

Open Science Fair

Menelaos Sotiriou talks about innovative dissemination in the context of NUCLEUS project & theatrical workshops. Workshop title: Innovative dissemination practices & Altmetrics Workshop abstact: The goal of the workshop is to further the understanding of innovative dissemination practices in open science and their relationship with altmetrics. In the first part of the workshop, OpenUP project researchers will give an overview of an innovative dissemination framework. The framework describes good practices and gives recommendations on how to create a successful research dissemination strategy beyond traditional academic dissemination. A special focus will lie on how to reach target audiences beyond the research community (e.g. business or the general public). Participants will be able to test the framework and a toolbox based on their dissemination needs and to give feedback in a discussion that involves the perspective of all stakeholders of dissemination and assessment (researchers and research organizations, funders, policy makers, journalists, practitioners & businesses etc.). In the second part, we will present a taxonomy linking channels of dissemination and altmetrics indicators. In between, we will present best practice examples of innovative dissemination. DAY 2 - PARALLEL SESSION 3 http://opensciencefair.eu/workshops/parallel-day-2-1/innovative-dissemination-practices-and-altmetrics

Similar to OSFair2017 Workshop | West-Life: world-wide e-infrastructure for structural biology

Big data from small data: A survey of the neuroscience landscape through the...

Maryann Martone

Bioinformatics t1-introduction wim-vancriekinge_v2013

Prof. Wim Van Criekinge

DR KL CV v5Γενικό Λύκειο Σκύδρας

Introduction to Systemics with focus on Systems Biology

Mrinal Vashisth

Bioinformatics__Lecture_1.ppt

sirwansleman

Ewan Birney Biocuration 2013

Iddo

How do we know what we don’t know: Using the Neuroscience Information Framew...

Maryann Martone

Mauricio carrillo trippguadalupe.moreno

2014 09 30_t1_bioinformatics_wim_vancriekinge

Prof. Wim Van Criekinge

Computer science history.pdf

sirwansleman

RDAP14: Maryann Martone, Keynote, The Neuroscience Information Framework

ASIS&T

Overview of cheminformatics

Benjamin Bucior

Biological databases

SEKHARREDDYAMBATI

Neuroscience as networked science

Neuroscience Information Framework

Biological Database (1)pptxpdfpdfpdf.pdf

BioinformaticsCentre

485 lec3 history_review_ii

hhalhaddad

A knowledge capture framework for domain specific search systems

ramakanz

Introduction to Bioinformatics

jaumebp

Clustering the royal society of chemistry chemical repository to enable enhan...

Valery Tkachenko

2015 bioinformatics wim_vancriekinge

Prof. Wim Van Criekinge

Similar to OSFair2017 Workshop | West-Life: world-wide e-infrastructure for structural biology (20)

Big data from small data: A survey of the neuroscience landscape through the...

Bioinformatics t1-introduction wim-vancriekinge_v2013

DR KL CV v5

Introduction to Systemics with focus on Systems Biology

Bioinformatics__Lecture_1.ppt

Ewan Birney Biocuration 2013

How do we know what we don’t know: Using the Neuroscience Information Framew...

Mauricio carrillo tripp

2014 09 30_t1_bioinformatics_wim_vancriekinge

Computer science history.pdf

RDAP14: Maryann Martone, Keynote, The Neuroscience Information Framework

Overview of cheminformatics

Biological databases

Neuroscience as networked science

Biological Database (1)pptxpdfpdfpdf.pdf

485 lec3 history_review_ii

A knowledge capture framework for domain specific search systems

Introduction to Bioinformatics

Clustering the royal society of chemistry chemical repository to enable enhan...

2015 bioinformatics wim_vancriekinge

More from Open Science Fair

OSFair2017 workshop | Monitoring open science trends in europe

Open Science Fair

OSFair2017 Worksop | NUCLEUS project - Are you ready to perform in RRI ecosys...

Open Science Fair

OSFair2017 Workshop | Data Analytics meets Social Sciences: New Frontiers of ...

Open Science Fair

Haris Papageorgiou talks about Data Analytics in Social Sciences Workshop title:TDM unlocking a goldmine of information Training overview: Text and Data Mining (TDM) is a natural ‘next step’ in open science. It can lead to new and unexpected discoveries and increase the impact of publications and repositories. This workshop showcases examples of successful TDM and infrastructural solutions for researchers. We will also discuss what is needed to make most of infrastructures and how publishers and repositories can open up their content. DAY 2 - PARALLEL SESSION 4 & 5

OSFair2017 Workshop | Building a global knowledge commons - ramping up reposi...

Open Science Fair

Eloy Rodrigues, Petr Knoth & Kathleen Shearer showcase the conceptual model for this vision, as well as the role and functions of repositories within this model. Workshop title: Building a global knowledge commons - ramping up repositories to support widespread change in the ecosystem Workshop abstract: The extensive international deployment of repository systems in higher education and research institutions, as well as scholarly communities, provides the foundation for a distributed, globally networked infrastructure for scholarly communication. This distributed network of repositories can and should be a powerful tool to promote the transformation of the scholarly communication ecosystem. However, repository platforms are still using technologies and protocols designed almost twenty years ago, before the boom of the web and the dominance of Google, social networking, semantic web and ubiquitous mobile devices. In April 2016, the Confederation of Open Access Repositories (COAR) launched a working group to help identify new functionalities and technologies for repositories and develop a road map for their adoption. For the past several months, the group has been working to define a vision for repositories and sketch out the priority user stories and scenarios that will help guide the development of new functionalities. The results of this work will be available in the summer of 2017. This workshop will present the functionalities and technologies for the next generation of repositories and reflect on how these functionalities will be adopted into the existing software platforms. In addition, participants will discuss the important implications for the network layers, and how repositories will uniformly interact with the networks to provide value added services on top of their content. DAY 3 - PARALLEL SESSION 6 & 7 http://www.opensciencefair.eu/workshops/parallel-day-3-1/building-a-global-knowledge-commons-ramping-up-repositories-to-support-widespread-change-in-the-ecosystem

OSFair2017 Workshop | Research lifecycle in Arts, Humanities and Social Sciences

Open Science Fair

Agiatis Benardou, Caroline Sutton & Janet Remington talk about the research lifecycle in Arts, Humanities & Social Sciences Workshop title: Research lifecycles in the humanities and social sciences Workshop abstract: A host of initiatives have moved the open agenda beyond simply open access to journal articles or monographs to a consideration of the entire research lifecycle and points at which this can be opened up. Further, we are entering a second phase of open scholarship whereby the community is now seeking to link together the many scattered solutions for different pieces of the research lifecycle. Open Scholarship offers an important opportunity for scholars in the social sciences and humanities. Although open access has gained traction more recently, it is well-known that widespread adoption of and transition to open access to journals and monographs has lagged behind many other subject areas for a host of reasons. Engaging scholars in these subject areas in open scholarship more broadly offers and opportunity to approach open from a multitude of angles. However, the research lifecycle that is presented and visualized by those engaged in open science typically visualises that of a scientist working within STEM fields. This follows an expected pattern (e.g. planning, implementation, publishing, discovery and impact, preservation, re-use) or sets of patterns in the form of sub-cycles (e.g. planning cycle, project cycle, publication cycle, preservation cycle, impact). These visualisations do not align with the process of scholarly inquiry that many humanities scholars and qualitative social scientists are engaged in and risks marginalising some communities. Imagine a professor of music, who creates bits of initially unrelated compositions and harmonies, which arose out of inspiration derived from listening to a gentle brook. These might give rise to new understandings of former theories of music or push forward techniques. The aim of this workshop is to work together with scholars to identify a series of research workflows that better reflect the processes of scholarship in the humanities and social sciences. Once lifecycles are drafted, participants will identify points of potential sharing and open opportunities. These points will then be associated with current solutions and gaps will be identified. DAY 1 - PARALLEL SESSION 2 http://opensciencefair.eu/workshops/parallel-day-1-2/research-lifecycles-in-the-humanities-and-social-sciences

OSFair2017 Workshop | Towards a Policy Framework for the European Open Scienc...

Open Science Fair

Workshop title: Towards a Policy Framework for the European Open Science Cloud Workshop abstract: The workshop provides a hands on approach in relation both to the understanding of the EU open science policies and their application by related stakeholders. It will seek to explore, propose and test different aspects of policy documents created by and for different types of stakeholders (e.g. RPOs, funders, policy makers etc) in the context of EOSC. Drawing on the work by the EOSC policy work, the workshop invites participants to bring their own policies or work on model policies to develop a simple but comprehensive policy document tailored to their needs and conforming to the EU policy and legal framework. It is useful to the broader Open Science community as it brings together services, stakeholders and policies and allows for a better understanding of the interaction between different constituencies. DAY 2 - PARALLEL SESSION 3

OSFair2017 Workshop | Text mining

Open Science Fair

Manuel Noya talks about the science-industry relationship driven by competitive intelligence and how to surf emerging technologies Workshop title:TDM unlocking a goldmine of information Training overview: Text and Data Mining (TDM) is a natural ‘next step’ in open science. It can lead to new and unexpected discoveries and increase the impact of publications and repositories. This workshop showcases examples of successful TDM and infrastructural solutions for researchers. We will also discuss what is needed to make most of infrastructures and how publishers and repositories can open up their content. DAY 2 - PARALLEL SESSION 4 & 5

OSFair2017 Workshop | EOSCpilot governance

Open Science Fair

Matthew Dovey & Jessica Parland-von Essen present EOSC governance & objectives. Workshop title: Open Science policy in the context of EOSC governance framework Workshop overview: The challenge of EOSC governance is how to construct a framework allowing varied and disparate stakeholders to work together. The EOSCPilot project has established a Governance Development Forum (EGDF) so that all stakeholders can contribute to the development of a governance framework to inform the establishment of EOSC and its governance structure. In this workshop we will discuss how Open Science should manifest in the EOSC governance framework. When: DAY 2 - PARALLEL SESSION 4

OSFair2017 Workshop | Brokering services facilitating interoperability and da...

Open Science Fair

Stefano Nativi presents the RDA. Workshop title: Organising high-quality research data management services Workshop abstract: Open science needs high quality data management where researchers can create, use and share data according to well defined standards and practices. this is one of the pillars of Open Science. In the data management landscape we find quite a few organisations that aim at achieving this, however to get it right, a collaboration is called for where all can play a suitable role and present this in a consistent way to the researcher. The proposed workshop brings together representatives of standard organisation (RDA), eInfrastructures (EUDAT) and Libraries (LIBER) that together can organise the high quality data management for research. DAY 1 - PARALLEL SESSION 2 http://opensciencefair.eu/workshops/organising-high-quality-research-data-management-services

OSFair2017 Workshop | Service provisioning for excellent sciences

Open Science Fair

Daan Broeder presents the EUDAT community Workshop title: Organising high-quality research data management services Workshop abstract: Open science needs high quality data management where researchers can create, use and share data according to well defined standards and practices. this is one of the pillars of Open Science. In the data management landscape we find quite a few organisations that aim at achieving this, however to get it right, a collaboration is called for where all can play a suitable role and present this in a consistent way to the researcher. The proposed workshop brings together representatives of standard organisation (RDA), eInfrastructures (EUDAT) and Libraries (LIBER) that together can organise the high quality data management for research. DAY 1 - PARALLEL SESSION 2 http://opensciencefair.eu/workshops/organising-high-quality-research-data-management-services

OSFair2017 Theatrical Workshop | Are you ready to perform in the rri ecosystem

Open Science Fair

Alexandros Koukovinis & Menelaos Sotiriou present the performance chapters. Workshop abstract: This workshop highlights the concept of a Support and Coordination H2020 action, namely NUCLEUS, which is targeted on Responsible Research and Innovation. It is aligned with the overall objective of the OSFair conference, answering to the impact of open science/novel ways of disseminating science. What NUCLEUS project introduces, is that based on a common understanding that science and innovation are driving forces of sustainable and inclusive societies around the world, it will develop new cultural and organisational approaches allowing universities to better respond and react to societal needs and challenges. To pursue this goal NUCLEUS will develop, support and implement inclusive and sustainable approaches to “Responsible Research and Innovation” (RRI) within the governance and culture of European universities and research organisations. A wide scale implementation roadmap and a future of science with and for the society will be presented in the most engaging way. Day 1 - 17.30 http://opensciencefair.eu/theatrical-workshop-are-you-ready-to-perform-in-the-rri-ecosystem

OSFair2017 Theatrical Workshop | Nucleus H2020 EU project

Open Science Fair

Alexandros Koukovinis & Menelaos Sotiriou present the Nucleus H2020 project. Workshop abstract: This workshop highlights the concept of a Support and Coordination H2020 action, namely NUCLEUS, which is targeted on Responsible Research and Innovation. It is aligned with the overall objective of the OSFair conference, answering to the impact of open science/novel ways of disseminating science. What NUCLEUS project introduces, is that based on a common understanding that science and innovation are driving forces of sustainable and inclusive societies around the world, it will develop new cultural and organisational approaches allowing universities to better respond and react to societal needs and challenges. To pursue this goal NUCLEUS will develop, support and implement inclusive and sustainable approaches to “Responsible Research and Innovation” (RRI) within the governance and culture of European universities and research organisations. A wide scale implementation roadmap and a future of science with and for the society will be presented in the most engaging way. Day 1 - 17.30 http://opensciencefair.eu/theatrical-workshop-are-you-ready-to-perform-in-the-rri-ecosystem

OSFair2017 Workshop | Open Knowledge Maps, A visual interface to the world's ...

Open Science Fair

Peter Kraker & Rainer Bachleitner make an introduction to Open Knowledge Maps Workshop abstract: This tutorial introduces participants to an innovative discovery tool that is built on top of the open science infrastructure. It showcases the value of open for all stakeholders beyond open access to research outputs. Participants will go on a scientific scavenger hunt in an unknown research field that is intended to improve their own discovery process, including ample time for feedback and discussion. DAY 3 - PARALLEL SESSION 8 http://opensciencefair.eu/training/parallel-day-3-3/visual-discovery-with-open-knowledge-maps

OSFair2017 Training | Reproducibility in critical care research

Open Science Fair

Tom Pollard talks about reproducibility in critical care research & makes an introduction to MIMIC, the eICU Collaborative Research Database and datathons Workshop title: Datathons in Evidence-Based Medicine: Applying Open Science Principles to Support Cross-Disciplinary Education and Research Workshop abstract: In this interactive workshop, we explore how open science enables “datathons”, events that bring together teams of researchers to work together on unanswered clinical questions. We begin by outlining the datathon model and describe our experiences in holding these events internationally. We then offer an opportunity to participate in an interactice exercise, working together to analyse highly detailed information collected from patients admitted to critical care units at a large tertiary care hospital. Participants will learn about open science in clinical research and gain an overview of MIMIC-III, a freely-available critical care dataset collected from over >50,000 hospital stays. DAY 2 - PARALLEL SESSION 3 http://opensciencefair.eu/training/parallel-day-2-1/datathons-in-evidence-based-medicine-applying-open-science-principles-to-support-cross-disciplinary-education-and-research

OSFair2017 Training | Big data and evidence-based medicine in Greece

Open Science Fair

Lefteris Thireos talks about big data and evidence-based medicine in Greece. Workshop title: Datathons in Evidence-Based Medicine: Applying Open Science Principles to Support Cross-Disciplinary Education and Research Workshop abstract: In this interactive workshop, we explore how open science enables “datathons”, events that bring together teams of researchers to work together on unanswered clinical questions. We begin by outlining the datathon model and describe our experiences in holding these events internationally. We then offer an opportunity to participate in an interactice exercise, working together to analyse highly detailed information collected from patients admitted to critical care units at a large tertiary care hospital. Participants will learn about open science in clinical research and gain an overview of MIMIC-III, a freely-available critical care dataset collected from over >50,000 hospital stays. DAY 2 - PARALLEL SESSION 3 http://opensciencefair.eu/training/parallel-day-2-1/datathons-in-evidence-based-medicine-applying-open-science-principles-to-support-cross-disciplinary-education-and-research

OSFair2017 Training | What is Open Science and why should I care?

Open Science Fair

Nancy Pontika talks about opening up science & implementation. Workshop title: Fostering the practical implementation of Open Science in Horizon 2020 and beyond Workshop overview: This workshop will showcase some of the elements required for the transition to Open Science: services and tools, policies as guidance for good practices, and the roles of the respective actors and their networks. DAY 2 - PARALLEL SESSION 4 & 5

OSFair2017 Training | OpenAIRE monitoring services, EC FP7 & H2020 & other na...

Open Science Fair

Pedro Principe presents OpenAIRE monitoring services. Workshop title: Fostering the practical implementation of Open Science in Horizon 2020 and beyond Workshop overview: This workshop will showcase some of the elements required for the transition to Open Science: services and tools, policies as guidance for good practices, and the roles of the respective actors and their networks. DAY 2 - PARALLEL SESSION 4 & 5

OSFair2017 Training | Designing & implementing open access, open data & open ...

Open Science Fair

Eloy Rodrigues, José Carvalho & Pedro Príncipe talk about designing & implementing Open Access, Open Data & Open Science policies. Workshop title: Fostering the practical implementation of Open Science in Horizon 2020 and beyond Workshop overview: This workshop will showcase some of the elements required for the transition to Open Science: services and tools, policies as guidance for good practices, and the roles of the respective actors and their networks. DAY 2 - PARALLEL SESSION 4 & 5

OSFair2017 Training | Best practice in Open Science

Open Science Fair

Iryna Kuchma talks about best practices in Open Science. Workshop title: Fostering the practical implementation of Open Science in Horizon 2020 and beyond Workshop overview: This workshop will showcase some of the elements required for the transition to Open Science: services and tools, policies as guidance for good practices, and the roles of the respective actors and their networks. DAY 2 - PARALLEL SESSION 4 & 5

OSFair2017 Worksop | Innovative dissemination practices & Altmetrics

Open Science Fair

Peter Kraker, Michela Vignoli & Rainer Bachleitner give an overview of an innovative dissemination framework & present the OpenUP Innovative Dissemination Toolbox. Workshop title: Innovative dissemination practices & Altmetrics Workshop abstact: The goal of the workshop is to further the understanding of innovative dissemination practices in open science and their relationship with altmetrics. In the first part of the workshop, OpenUP project researchers will give an overview of an innovative dissemination framework. The framework describes good practices and gives recommendations on how to create a successful research dissemination strategy beyond traditional academic dissemination. A special focus will lie on how to reach target audiences beyond the research community (e.g. business or the general public). Participants will be able to test the framework and a toolbox based on their dissemination needs and to give feedback in a discussion that involves the perspective of all stakeholders of dissemination and assessment (researchers and research organizations, funders, policy makers, journalists, practitioners & businesses etc.). In the second part, we will present a taxonomy linking channels of dissemination and altmetrics indicators. In between, we will present best practice examples of innovative dissemination. DAY 2 - PARALLEL SESSION 3 http://opensciencefair.eu/workshops/parallel-day-2-1/innovative-dissemination-practices-and-altmetrics License: CC-BY, unless otherwise noted

More from Open Science Fair (20)

OSFair2017 workshop | Monitoring open science trends in europe

OSFair2017 Worksop | NUCLEUS project - Are you ready to perform in RRI ecosys...

OSFair2017 Workshop | Data Analytics meets Social Sciences: New Frontiers of ...

OSFair2017 Workshop | Building a global knowledge commons - ramping up reposi...

OSFair2017 Workshop | Research lifecycle in Arts, Humanities and Social Sciences

OSFair2017 Workshop | Towards a Policy Framework for the European Open Scienc...

OSFair2017 Workshop | Text mining

OSFair2017 Workshop | EOSCpilot governance

OSFair2017 Workshop | Brokering services facilitating interoperability and da...

OSFair2017 Workshop | Service provisioning for excellent sciences

OSFair2017 Theatrical Workshop | Are you ready to perform in the rri ecosystem

OSFair2017 Theatrical Workshop | Nucleus H2020 EU project

OSFair2017 Workshop | Open Knowledge Maps, A visual interface to the world's ...

OSFair2017 Training | Reproducibility in critical care research

OSFair2017 Training | Big data and evidence-based medicine in Greece

OSFair2017 Training | What is Open Science and why should I care?

OSFair2017 Training | OpenAIRE monitoring services, EC FP7 & H2020 & other na...

OSFair2017 Training | Designing & implementing open access, open data & open ...

OSFair2017 Training | Best practice in Open Science

OSFair2017 Worksop | Innovative dissemination practices & Altmetrics

Recently uploaded

Phenomics assisted breeding in crop improvement

IshaGoswami9

As the population is increasing and will reach about 9 billion upto 2050. Also due to climate change, it is difficult to meet the food requirement of such a large population. Facing the challenges presented by resource shortages, climate change, and increasing global population, crop yield and quality need to be improved in a sustainable way over the coming decades. Genetic improvement by breeding is the best way to increase crop productivity. With the rapid progression of functional genomics, an increasing number of crop genomes have been sequenced and dozens of genes influencing key agronomic traits have been identified. However, current genome sequence information has not been adequately exploited for understanding the complex characteristics of multiple gene, owing to a lack of crop phenotypic data. Efficient, automatic, and accurate technologies and platforms that can capture phenotypic data that can be linked to genomics information for crop improvement at all growth stages have become as important as genotyping. Thus, high-throughput phenotyping has become the major bottleneck restricting crop breeding. Plant phenomics has been defined as the high-throughput, accurate acquisition and analysis of multi-dimensional phenotypes during crop growing stages at the organism level, including the cell, tissue, organ, individual plant, plot, and field levels. With the rapid development of novel sensors, imaging technology, and analysis methods, numerous infrastructure platforms have been developed for phenotyping.

Topic: SICKLE CELL DISEASE IN CHILDREN-3.pdf

TinyAnderson

Chapter 12 - climate change and the energy crisis

tonzsalvador2222

DMARDs Pharmacolgy Pharm D 5th Semester.pdf

fafyfskhan251kmf

Leaf Initiation, Growth and Differentiation.pdf

RenuJangid3

Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...

University of Maribor

原版制作(carleton毕业证书)卡尔顿大学毕业证硕士文凭原版一模一样

yqqaatn0

原版纸张【微信：741003700 】【(carleton毕业证书)卡尔顿大学毕业证】【微信：741003700 】学位证，留信认证（真实可查，永久存档）offer、雅思、外壳等材料/诚信可靠,可直接看成品样本，帮您解决无法毕业带来的各种难题！外壳，原版制作，诚信可靠，可直接看成品样本。行业标杆！精益求精，诚心合作，真诚制作！多年品质 ,按需精细制作，24小时接单,全套进口原装设备。十五年致力于帮助留学生解决难题，包您满意。本公司拥有海外各大学样板无数，能完美还原海外各大学 Bachelor Diploma degree, Master Degree Diploma 1:1完美还原海外各大学毕业材料上的工艺：水印，阴影底纹，钢印LOGO烫金烫银，LOGO烫金烫银复合重叠。文字图案浮雕、激光镭射、紫外荧光、温感、复印防伪等防伪工艺。材料咨询办理、认证咨询办理请加学历顾问Q/微741003700 留信网认证的作用: 1:该专业认证可证明留学生真实身份 2:同时对留学生所学专业登记给予评定 3:国家专业人才认证中心颁发入库证书 4:这个认证书并且可以归档倒地方 5:凡事获得留信网入网的信息将会逐步更新到个人身份内，将在公安局网内查询个人身份证信息后，同步读取人才网入库信息 6:个人职称评审加20分 7:个人信誉贷款加10分 8:在国家人才网主办的国家网络招聘大会中纳入资料，供国家高端企业选择人才

Deep Software Variability and Frictionless Reproducibility

University of Rennes, INSA Rennes, Inria/IRISA, CNRS

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

NuGOweek 2024 Ghent programme overview flyer

pablovgd

ESR spectroscopy in liquid food and beverages.pptx

PRIYANKA PATEL

With increasing population, people need to rely on packaged food stuffs. Packaging of food materials requires the preservation of food. There are various methods for the treatment of food to preserve them and irradiation treatment of food is one of them. It is the most common and the most harmless method for the food preservation as it does not alter the necessary micronutrients of food materials. Although irradiated food doesn’t cause any harm to the human health but still the quality assessment of food is required to provide consumers with necessary information about the food. ESR spectroscopy is the most sophisticated way to investigate the quality of the food and the free radicals induced during the processing of the food. ESR spin trapping technique is useful for the detection of highly unstable radicals in the food. The antioxidant capability of liquid food and beverages in mainly performed by spin trapping technique.

Seminar of U.V. Spectroscopy by SAMIR PANDA

SAMIR PANDA

ANAMOLOUS SECONDARY GROWTH IN DICOT ROOTS.pptx

RASHMI M G

Shallowest Oil Discovery of Turkiye.pptx

Gokturk Mehmet Dilci

Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...

Sérgio Sacani

Since volcanic activity was first discovered on Io from Voyager images in 1979, changes on Io’s surface have been monitored from both spacecraft and ground-based telescopes. Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images show that a plume deposit from a powerful eruption at Pillan Patera has covered part of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive optics at visible wavelengths.

bordetella pertussis.................................ppt

kejapriya1

Introduction to Mean Field Theory(MFT).pptx

zeex60

Lateral Ventricles.pdf very easy good diagrams comprehensive

silvermistyshot

Mudde & Rovira Kaltwasser. - Populism - a very short introduction [2017].pdf

frank0071

platelets_clotting_biogenesis.clot retractionpptx

muralinath2

Orion Air Quality Monitoring Systems - CWS

Columbia Weather Systems

Recently uploaded (20)

Phenomics assisted breeding in crop improvement

Topic: SICKLE CELL DISEASE IN CHILDREN-3.pdf

Chapter 12 - climate change and the energy crisis

DMARDs Pharmacolgy Pharm D 5th Semester.pdf

Leaf Initiation, Growth and Differentiation.pdf

Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...

原版制作(carleton毕业证书)卡尔顿大学毕业证硕士文凭原版一模一样

Deep Software Variability and Frictionless Reproducibility

NuGOweek 2024 Ghent programme overview flyer

ESR spectroscopy in liquid food and beverages.pptx

Seminar of U.V. Spectroscopy by SAMIR PANDA

ANAMOLOUS SECONDARY GROWTH IN DICOT ROOTS.pptx

Shallowest Oil Discovery of Turkiye.pptx

Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...

bordetella pertussis.................................ppt

Introduction to Mean Field Theory(MFT).pptx

Lateral Ventricles.pdf very easy good diagrams comprehensive

Mudde & Rovira Kaltwasser. - Populism - a very short introduction [2017].pdf

platelets_clotting_biogenesis.clot retractionpptx

Orion Air Quality Monitoring Systems - CWS

OSFair2017 Workshop | West-Life: world-wide e-infrastructure for structural biology

1. West-Life: World-wide E-infrastructure for structural biology Chris Morris, STFC

2. Outlook • Structural biology aims to understand the molecular basis of life • Experimental centres – Synchrotrons (MX), 47 in world – Electron microscopes (EM), rapid growth – Nuclear Magnetic Resonance (NMR) instruments, ~200 in Europe – A long tail of other techniques • Researchers in every university – And in pharmaceutical companies – Around 25,000 structural experiments per year

3. Scientific Process • Identify a protein of interest (“target”) • Make recombinant DNA (“construct”) • Express in E.Coli or other tractable culture • Purify • Can crystallize? MX • Can’t crystallize? EM, NMR etc • Determine structure using software tools – Automatic for simpler MX structures – Months of guided computation for some EM structures • Publish… Sample Prep.

4. Scholarly communication practices • Literature – Life Sciences papers are often open access • Datasets: – Final structure is deposited in Protein Data Bank – Intermediate data too • Software suites and services – CCP4, Phenix, weNMR – Rapid developments for EM PDB new entries / year (log scale)

5. Scholarly communication desiderata • Archiving experimental data – Some progress, but 100M for MX, 1TB for EM – XFEL a firehose – full access for reviewers • Full provenance, structure to sample – Reproducibility of sample prep is poor • Reproducibility of processing – PDB-REDO reprocesses with latest algorithms • Automatic acquisition of metadata – Scientists don’t like housekeeping

6. For more detail… The Life Cycle of Structural Biology Data https://www.rd-alliance.org/group/structural-biology- ig/outcomes/life-cycle-structural-biology-data Corresponding author: Chris Morris Contributors: Claudia Alen, Lucia Banci, Alexandre Bonvin, Pablo Conesa, Alfonso Duarte, John Helliwell, Rob Hooft, Brian Matthews, Antonio Rosato, Sameer Velankar, Geerten Vuister, John Westbrook, Martyn Winn

OSFair2017 Workshop | West-Life: world-wide e-infrastructure for structural biology

Recommended

Recommended

More Related Content

Similar to OSFair2017 Workshop | West-Life: world-wide e-infrastructure for structural biology

Similar to OSFair2017 Workshop | West-Life: world-wide e-infrastructure for structural biology (20)

More from Open Science Fair

More from Open Science Fair (20)

Recently uploaded

Recently uploaded (20)

OSFair2017 Workshop | West-Life: world-wide e-infrastructure for structural biology