scholarly journals Adapting federated cyberinfrastructure for shared data collection facilities in structural biology

2012 ◽  
Vol 19 (3) ◽  
pp. 462-467 ◽  
Author(s):  
Ian Stokes-Rees ◽  
Ian Levesque ◽  
Frank V. Murphy ◽  
Wei Yang ◽  
Ashley Deacon ◽  
...  
Keyword(s):  
Data Collection ◽  
Structural Biology ◽  
Shared Data

scholarly journals Getting Started Creating Data Dictionaries: How to Create a Shareable Data Set

2021 ◽  
Vol 4 (1) ◽  
pp. 251524592092800
Author(s):  
Erin M. Buchanan ◽  
Sarah E. Crain ◽  
Ari L. Cunningham ◽  
Hannah R. Johnson ◽  
Hannah Stash ◽  
...  
Keyword(s):  
Data Collection ◽  
Data Sharing ◽  
Search Engine ◽  
Web Applications ◽  
Data Sets ◽  
Data Dictionary ◽  
Data Set ◽  
Entire Process ◽  
Shared Data ◽  
Source Data

As researchers embrace open and transparent data sharing, they will need to provide information about their data that effectively helps others understand their data sets’ contents. Without proper documentation, data stored in online repositories such as OSF will often be rendered unfindable and unreadable by other researchers and indexing search engines. Data dictionaries and codebooks provide a wealth of information about variables, data collection, and other important facets of a data set. This information, called metadata, provides key insights into how the data might be further used in research and facilitates search-engine indexing to reach a broader audience of interested parties. This Tutorial first explains terminology and standards relevant to data dictionaries and codebooks. Accompanying information on OSF presents a guided workflow of the entire process from source data (e.g., survey answers on Qualtrics) to an openly shared data set accompanied by a data dictionary or codebook that follows an agreed-upon standard. Finally, we discuss freely available Web applications to assist this process of ensuring that psychology data are findable, accessible, interoperable, and reusable.

A COOPERATIVE APPROACH FOR MEASURING DIRECT-USE DAMAGES: THE 1992 AVILA BEACH (CALIFORNIA) OIL SPILL

1995 ◽  
Vol 1995 (1) ◽  
pp. 327-331
Author(s):  
Richard W. Dunford ◽  
Kristy E. Mathews ◽  
H. Spencer Banzhaf
Keyword(s):  
Data Collection ◽  
Oil Spill ◽  
Natural Resource ◽  
The State ◽  
Damage Estimation ◽  
Cooperative Approach ◽  
Shared Data ◽  
Reduced Costs ◽  
Oil Company ◽  
Direct Use

ABSTRACT A cooperative approach was used to estimate natural resource damages from the Avila Beach, California, spill. The approach was cooperative because we, on behalf of Union Oil Company of California (UNOCAL), and the economist working for the State of California shared data collection and damage estimation responsibilities. Cooperative assessments have several advantages, including reduced costs and less duplication. Because this case was not settled when this paper was submitted, we provide no damage estimates.

scholarly journals Beamline automation and mail-in data collection at SPring-8 structural biology beamlines

2008 ◽  
Vol 64 (a1) ◽  
pp. C177-C177
Author(s):  
G. Ueno ◽  
K. Hasegawa ◽  
N. Okazaki ◽  
H. Murakami ◽  
T. Hikima ◽  
...  
Keyword(s):  
Data Collection ◽  
Structural Biology

scholarly journals Identifying, studying and making good use of macromolecular crystals

2014 ◽  
Vol 70 (8) ◽  
pp. 993-1008 ◽  
Author(s):  
Guillermo Calero ◽  
Aina E. Cohen ◽  
Joseph R. Luft ◽  
Janet Newman ◽  
Edward H. Snell
Keyword(s):  
Data Collection ◽  
Visible Light ◽  
Structural Biology ◽  
Protein Structures ◽  
Data Bank ◽  
Potential Outcomes ◽  
Structural Knowledge ◽  
X Ray ◽  
X Ray Crystallography ◽  
Molecular Scale

Structural biology has contributed tremendous knowledge to the understanding of life on the molecular scale. The Protein Data Bank, a depository of this structural knowledge, currently contains over 100 000 protein structures, with the majority stemming from X-ray crystallography. As the name might suggest, crystallography requires crystals. As detectors become more sensitive and X-ray sources more intense, the notion of a crystal is gradually changing from one large enough to embellish expensive jewellery to objects that have external dimensions of the order of the wavelength of visible light. Identifying these crystals is a prerequisite to their study. This paper discusses developments in identifying these crystals during crystallization screening and distinguishing them from other potential outcomes. The practical aspects of ensuring that once a crystal is identified it can then be positioned in the X-ray beam for data collection are also addressed.

scholarly journals Development and Evaluation of Two Integrated Care Models for Children Using a Partnered Formative Evaluation Approach

2018 ◽  
Vol 28 (Supp) ◽  
pp. 445-456 ◽  
Author(s):  
Bonnie T. Zima ◽  
Michael McCreary ◽  
Kristen Kenan ◽  
Michelle Churchey-Mims ◽  
Hannah Chi ◽  
...  
Keyword(s):  
Cohort Study ◽  
Data Collection ◽  
Integrated Care ◽  
Formative Evaluation ◽  
Private Foundation ◽  
Shared Data ◽  
Evaluation Approach ◽  
Care Models ◽  
Data Collection Approach ◽  
Integrated Care Models

Objective: To describe the development and evaluation of two integrated care mod­els using a partnered formative evaluation approach across a private foundation, clinic leaders, providers and staff, and a universi­ty-based research center.Design: Retrospective cohort study using multiple data sources.Setting: Two federal qualified health care centers serving low-income children and families in Chicago.Participants: Private foundation, clinic and academic partners.Interventions: Development of two inte­grated care models and partnered evalua­tion design.Main Outcome Measures: Accomplish­ments and early lessons learned.Results: Together, the foundation-clinic-academic partners worked to include best practices in two integrated care models for children while developing the evaluation design. A shared data collection approach, which empowered the clinic partners to collect data using a web-based tool for a prospective longitudinal cohort study, was also created.Conclusion: Across three formative evalua­tion stages, the foundation, clinic, and aca­demic partners continued to reach beyond their respective traditional roles of project oversight, clinical service, and research as adjustments were collectively made to accommodate barriers and unanticipated events. Together, an innovative shared data collection approach was developed that extends partnered research to include data collection being led by the clinic partners and supported by the technical resources of a university-based research center.Ethn Dis. 2018;28(Suppl 2):445-456; doi:10.18865/ed.28.S2.445.

scholarly journals Energy optimization of a regular macromolecular crystallography beamline for ultra-high-resolution crystallography

2015 ◽  
Vol 22 (1) ◽  
pp. 172-174 ◽  
Author(s):  
Gerd Rosenbaum ◽  
Stephan L. Ginell ◽  
Julian C.-H. Chen
Keyword(s):  
High Resolution ◽  
Data Collection ◽  
Structural Biology ◽  
Practical Method ◽  
Accurate Data ◽  
Macromolecular Crystallography ◽  
X Ray ◽  
Standard Operating ◽  
Photon Source ◽  
Synchrotron Beamlines

A practical method for operating existing undulator synchrotron beamlines at photon energies considerably higher than their standard operating range is described and applied at beamline 19-ID of the Structural Biology Center at the Advanced Photon Source enabling operation at 30 keV. Adjustments to the undulator spectrum were critical to enhance the 30 keV flux while reducing the lower- and higher-energy harmonic contamination. A Pd-coated mirror and Al attenuators acted as effective low- and high-bandpass filters. The resulting flux at 30 keV, although significantly lower than with X-ray optics designed and optimized for this energy, allowed for accurate data collection on crystals of the small protein crambin to 0.38 Å resolution.

scholarly journals New opportunities in structural biology with XFEL: from sources to structures

2014 ◽  
Vol 70 (a1) ◽  
pp. C19-C19
Author(s):  
Soichi Wakatsuki
Keyword(s):  
Data Collection ◽  
Radiation Damage ◽  
Structural Biology ◽  
Single Particle ◽  
De Novo ◽  
Reconstruction Algorithm ◽  
Simultaneous Recording ◽  
Atomic Resolution ◽  
X Ray ◽  
Biology Research

X-ray free electron lasers (XFEL) have shown the promise of providing new opportunities in structural biology research with their extremely high peak brilliance and short pulses. It is reaching the stage where biologically important questions can be tackled using XFEL based on the "diffract-before-destroy" concept. The first part of this presentation will focus on macromolecular crystallography using XFEL with results obtained at LCLS so far and future scope. R&D efforts being pursued at SLAC/LCLS include new beam modes, (two-color beam for de novo phasing, wider bandwidth for SAXS/WAXS and spectroscopy), beam multiplexing, a dedicated new station for in-air data collection, next generation detectors, data analysis incorporating pulse-by-pulse spectrometer measurements and post refinement. These projects are being pursued in collaboration with many groups locally and globally with a goal to provide integrated facilities for cutting edge structural biology research. For example, two-color self-seeded XFEL mode is being developed for simultaneous recording of diffraction data at two energies in order to optimize the dispersive difference between the two wavelengths for phasing. Another area of collaborative effort is a development of dedicated station for in-air data collection with a variety of sample delivery schemes. The second part will discuss a possible roadmap towards atomic resolution single particle imaging using XFEL. Here, key questions are ·Can XFEL single particle 3D structural analysis at atomic resolution be done? ·What is the pulse characteristics required? ·Can we overcome the radiation damage at soft X-ray regime? ·What is the highest resolution attainable in comparison with cryoEM? A workshop at LCLS is being organized to discuss these questions in 4 areas: radiation damage, image reconstruction algorithm, beam modes and instrumentation, sample delivery and heterogeneity. The outcome of the workshop and follow-up discussions will be presented.

scholarly journals Assessing the JEOL CRYO ARM 300 for high-throughput automated single-particle cryo-EM in a multiuser environment

IUCrJ ◽  
2020 ◽  
Vol 7 (4) ◽  
pp. 707-718
Author(s):  
Marcus Fislage ◽  
Alexander V. Shkumatov ◽  
Annelore Stroobants ◽  
Rouslan G. Efremov
Keyword(s):  
High Resolution ◽  
Data Collection ◽  
Structural Biology ◽  
High Throughput ◽  
Single Particle ◽  
Illumination System ◽  
Resolution Electron ◽  
Access Mode ◽  
User Access ◽  
And Performance

Single-particle cryo-EM has become an indispensable structural biology method. It requires regular access to high-resolution electron cryogenic microscopes. To fully utilize the capacity of the expensive high-resolution instruments, the time used for data acquisition and the rate of data collection have to be maximized. This in turn requires high stability and high uptime of the instrument. One of the first 300 kV JEOL CRYO ARM 300 microscopes has been installed at the cryo-EM facility BECM at VIB-VUB, Brussels, where the microscope is used for continuous data collection on multiple projects. Here, the suitability and performance of the microscope is assessed for high-throughput single-particle data collection. In particular, the properties of the illumination system, the stage stability and ice contamination rates are reported. The microscope was benchmarked using mouse heavy-chain apoferritin which was reconstructed to a resolution of 1.9 Å. Finally, uptime and throughput statistics of the instrument accumulated during the first six months of the facility operation in user access mode are reported.

scholarly journals BioStruct-Africa: empowering Africa-based scientists through structural biology knowledge transfer and mentoring – recent advances and future perspectives

2019 ◽  
Vol 26 (5) ◽  
pp. 1843-1850
Author(s):  
Emmanuel Nji ◽  
Daouda A. K. Traore ◽  
Mama Ndi ◽  
Carolyn A. Joko ◽  
Declan A. Doyle
Keyword(s):  
Data Collection ◽  
Capacity Building ◽  
Structural Biology ◽  
Neglected Tropical Diseases ◽  
Protein Crystallization ◽  
Theoretical Background ◽  
New Drugs ◽  
African Continent ◽  
Synchrotron Light ◽  
Remote Data

Being able to visualize biology at the molecular level is essential for our understanding of the world. A structural biology approach reveals the molecular basis of disease processes and can guide the design of new drugs as well as aid in the optimization of existing medicines. However, due to the lack of a synchrotron light source, adequate infrastructure, skilled persons and incentives for scientists in addition to limited financial support, the majority of countries across the African continent do not conduct structural biology research. Nevertheless, with technological advances such as robotic protein crystallization and remote data collection capabilities offered by many synchrotron light sources, X-ray crystallography is now potentially accessible to Africa-based scientists. This leap in technology led to the establishment in 2017 of BioStruct-Africa, a non-profit organization (Swedish corporate ID: 802509-6689) whose core aim is capacity building for African students and researchers in the field of structural biology with a focus on prevalent diseases in the African continent. The team is mainly composed of, but not limited to, a group of structural biologists from the African diaspora. The members of BioStruct-Africa have taken up the mantle to serve as a catalyst in order to facilitate the information and technology transfer to those with the greatest desire and need within Africa. BioStruct-Africa achieves this by organizing workshops onsite at our partner universities and institutions based in Africa, followed by post-hoc online mentoring of participants to ensure sustainable capacity building. The workshops provide a theoretical background on protein crystallography, hands-on practical experience in protein crystallization, crystal harvesting and cryo-cooling, live remote data collection on a synchrotron beamline, but most importantly the links to drive further collaboration through research. Capacity building for Africa-based researchers in structural biology is crucial to win the fight against the neglected tropical diseases, e.g. ascariasis, hookworm, trichuriasis, lymphatic filariasis, active trachoma, loiasis, yellow fever, leprosy, rabies, sleeping sickness, onchocerciasis, schistosomiasis, etc., that constitute significant health, social and economic burdens to the continent. BioStruct-Africa aims to build local and national expertise that will have direct benefits for healthcare within the continent.

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