Participação no seminário Feminist Scholars Digital Workshop, promovido por Humanities, Arts, Science, and Techonology Alliance and Collaboratory (HASTAC): http://www.hastac.org/

This is a reprint from a paper published in the Proceedings of the IADIS International Conference 2009 IADIS Multi-Conference on Computer Science and Information Systems http://www.iadis.org; This paper presents the results achieved so far in the process of preparing the ground to develop a collaboratory in an Engineering R&D organization. This case study is part of a broader research project engaged in building a collaboratory in order to share knowledge and resources among the Portuguese State Laboratories. In the process of preparing the ground to develop the collaboratory in the first of the State Laboratories studied, an information audit was conducted and an online survey was launched. The survey targeted 240 people, including mainly professional researchers (c. 160), but also research trainees and some technical staff integrating the research teams. The questionnaire was designed so as to collect data on the information management and information culture of the organization, on the researchers’ information needs and information seeking, and on the information flows taking place, and was composed of two distinct and independent parts. The first obtained seventy nine responses, while the second achieved ninety two, corresponding to 33% and 38% of the total sample...

This paper presents the results achieved throughout the process of preparing the ground to develop a collaboratory in an Engineering R&D organization. This case study is part of a broader research project engaged in building a collaboratory in order to share knowledge and resources among the Portuguese State laboratories. In the process of preparing the ground to develop the collaboratory in the first of the laboratories studied, an information audit was conducted and an online survey was launched. The survey targeted 241 people, including mainly professional researchers, but also research trainees and some technical staff integrating the research teams. The questionnaire was designed so as to collect data on the organization’s information management and information culture, and on the information flows taking place, and their relationship with the objectives of the organization. The questionnaire comprised two distinct and independent parts. The first (on the organization’s information culture and information management) obtained seventy nine responses, while the second (information flows) achieved ninety two, corresponding to 32,8% and 38,2% of the total population, respectively. The work carried out provided the basic requirements for the task of developing a software infrastructure to support the collaboratory...

The RESID Database is a comprehensive collection of annotations and structures for protein post-translational modifications including N-terminal, C-terminal and peptide chain cross-link modifications. The RESID Database includes systematic and frequently observed alternate names, Chemical Abstracts Service registry numbers, atomic formulas and weights, enzyme activities, taxonomic range, keywords, literature citations with database cross-references, structural diagrams and molecular models. The NRL-3D Sequence–Structure Database is derived from the three-dimensional structure of proteins deposited with the Research Collaboratory for Structural Bioinformatics Protein Data Bank. The NRL-3D Database includes standardized and frequently observed alternate names, sources, keywords, literature citations, experimental conditions and searchable sequences from model coordinates. These databases are freely accessible through the National Cancer Institute–Frederick Advanced Biomedical Computing Center at these web sites: http://www.ncifcrf.gov/RESID, http://www.ncifcrf.gov/ NRL-3D; or at these National Biomedical Research Foundation Protein Information Resource web sites: http://pir.georgetown.edu/pirwww/dbinfo/resid.html...

The Protein Data Bank (PDB) is the central worldwide repository for three-dimensional (3D) structure data of biological macromolecules. The Research Collaboratory for Structural Bioinformatics (RCSB) has completely redesigned its resource for the distribution and query of 3D structure data. The re-engineered site is currently in public beta test at http://pdbbeta.rcsb.org. The new site expands the functionality of the existing site by providing structure data in greater detail and uniformity, improved query and enhanced analysis tools. A new key feature is the integration and searchability of data from over 20 other sources covering genomic, proteomic and disease relationships. The current capabilities of the re-engineered site, which will become the RCSB production site at http://www.pdb.org in late 2005, are described.

Based on a homology model of the Kv1.3 potassium channel, the recognitions of the six scorpion toxins, viz. agitoxin2, charybdotoxin, kaliotoxin, margatoxin, noxiustoxin, and Pandinus toxin, to the human Kv1.3 potassium channel have been investigated by using an approach of the Brownian dynamics (BD) simulation integrating molecular dynamics (MD) simulation. Reasonable three-dimensional structures of the toxin-channel complexes have been obtained employing BD simulations and triplet contact analyses. All of the available structures of the six scorpion toxins in the Research Collaboratory for Structural Bioinformatics Protein Data Bank determined by NMR were considered during the simulation, which indicated that the conformations of the toxin significantly affect both the molecular recognition and binding energy between the two proteins. BD simulations predicted that all the six scorpion toxins in this study use their β-sheets to bind to the extracellular entryway of the Kv1.3 channel, which is in line with the primary clues from the electrostatic interaction calculations and mutagenesis results. Additionally, the electrostatic interaction energies between the toxins and Kv1.3 channel correlate well with the binding affinities (−logKds)...

Multiple clinical informatics systems have been developed within separate departments of the University of Michigan Medical School. We are in the process of creating an “Honest Broker” method of safely and securely linking together data from different clinical systems for a research project studying the co-morbidity of depression and cardiovascular disease. The Michigan Clinical Research Collaboratory (MCRC) is an NIH/NHLBI Roadmap initiative funded to re-engineer the clinical research enterprise.

PURPOSE This case study describes a successful National Institutes of Health (NIH) Roadmap application that has created a new and innovative translational science partnership at the University of Michigan.

Due to its complex nature, modern biomedical research has become increasingly interdisciplinary and collaborative in nature. Although a necessity, interdisciplinary biomedical collaboration is difficult. There is, however, a growing body of literature on the study and fostering of collaboration in fields such as computer supported cooperative work (CSCW) and information science (IS). These studies of collaboration provide insight into how to potentially alleviate the difficulties of interdisciplinary collaborative research. We, therefore, undertook a cross cutting study of science and engineering collaboratories to identify emergent themes. We review many relevant collaboratory concepts: (a) general collaboratory concepts across many domains: communication, common workspace and coordination, and data sharing and management, (b) specific collaboratory concepts of particular biomedical relevance: data integration and analysis, security structure, metadata and data provenance, and interoperability and data standards, (c) environmental factors that support collaboratories: administrative and management structure, technical support, and available funding as critical environmental factors, and (d) future considerations for biomedical collaboration: appropriate training and long-term planning. In our opinion...

Modern biomedical research is evolving with the rapid growth of diverse data types, biophysical characterization methods, computational tools and extensive collaboration among researchers spanning various communities and having complementary backgrounds and expertise. Collaborating researchers are increasingly dependent on shared data and tools made available by other investigators with common interests, thus forming communities that transcend the traditional boundaries of the single research lab or institution. Barriers, however, remain to the formation of these virtual communities, usually due to the steep learning curve associated with becoming familiar with new tools, or with the difficulties associated with transferring data between tools. Recognizing the need for shared reference data and analysis tools, we are developing an integrated knowledge environment that supports productive interactions among researchers. Here we report on our current collaborative environment, which focuses on bringing together structural biologists working in the area of mass spectrometric based methods for the analysis of tertiary and quaternary macromolecular structures (MS3D) called the Collaboratory for MS3D (C-MS3D). C-MS3D is a web-portal designed to provide collaborators with a shared work environment that integrates data storage and management with data analysis tools. Files are stored and archived along with pertinent meta data in such a way as to allow file handling to be tracked (data provenance) and data files to be searched using keywords and modification dates. While at this time the portal is designed around a specific application...

As a collaboratory for cancer communication and education research, the National Cancer Institute’s (NCIs) Cancer Information Service (CIS) is in an ideal position to bridge the critical chasm that exists between service and research. This article describes the CIS’ current research program as well as the CIS Research Agenda launched in 2005. The CIS’ progress in developing and supporting recently funded studies that address this agenda is detailed. The unique resources and opportunities available to researchers, public health practitioners, health care providers, and community-based organizations interested in developing collaborative cancer communication and cancer education studies with the CIS are identified and described and an invitation to collaborate is extended.

Widespread sharing of data from electronic health records and patient-reported outcomes can strengthen the national capacity for conducting cost-effective clinical trials and allow research to be embedded within routine care delivery. While pragmatic clinical trials (PCTs) have been performed for decades, they now can draw on rich sources of clinical and operational data that are continuously fed back to inform research and practice. The Health Care Systems Collaboratory program, initiated by the NIH Common Fund in 2012, engages healthcare systems as partners in discussing and promoting activities, tools, and strategies for supporting active participation in PCTs. The NIH Collaboratory consists of seven demonstration projects, and seven problem-specific working group ‘Cores’, aimed at leveraging the data captured in heterogeneous ‘real-world’ environments for research, thereby improving the efficiency, relevance, and generalizability of trials. Here, we introduce the Collaboratory, focusing on its Phenotype, Data Standards, and Data Quality Core, and present early observations from researchers implementing PCTs within large healthcare systems. We also identify gaps in knowledge and present an informatics research agenda that includes identifying methods for the definition and appropriate application of phenotypes in diverse healthcare settings...

Regional SoTL collaboratories can provide a natural fit with political boundaries and funding opportunities; interconnections across regions can provide critical mass to sustain ongoing community interactions. It is unrealistic to expect these facilities to use a common technical platform or to adopt common social organizations, so a Framework for interconnection would be valuable. Our prototype Engagement Levels Framework includes four levels of faculty involvement, each with differing facilities to support research and knowledge mobilization: Cooperative Research Projects: Faculty who engage with a Teaching Research Collaboratory through specific short-term supported projects, as individuals and as teams, primarily focused on enhancing the learning experience and student success in their own courses and with some secondary focus on enhancing teaching practice for their colleagues at the institutional or provincial levels (and beyond). This secondary focus requires some effort to distinguish localized versus generalizable factors contributing to the success or limitations of an intervention in teaching. Practitioner/Researcher Core Communities: Faculty with an ongoing mutual engagement as a community, functioning both as an inquiry community to enhance the learning experience and student success in their own courses and as the core of a larger community of practitioner/researchers in research-led teaching...

We present the first report on an innovative new project named "RAD@home", a citizen-science research collaboratory built on free web-services like Facebook, Google, Skype, NASA Skyview, NED, TGSS etc.. This is the first of its kind in India, a zero-funded, zero-infrastructure, human-resource network to educate and directly involve in research, hundreds of science-educated under-graduate population of India, irrespective of their official employment and home-location with in the country. Professional international collaborators are involved in follow up observation and publication of the objects discovered by the collaboratory. We present here ten newly found candidate episodic radio galaxies, already proposed to GMRT, and ten more interesting cases which includes, bent-lobe radio galaxies located in new Mpc-scale filaments, likely tracing cosmological cluster accretion from the cosmic web. Two new Speca-like rare spiral-host large radio galaxies have also been been reported here. Early analyses from our follow up observations with the Subaru and XMM-Newton telescopes have revealed that Speca is likely a new entry to the cluster and is a fast rotating, extremely massive, star forming disk galaxy. Speca-like massive galaxies with giant radio lobes...

The National Fusion Collaboratory (NFC) project was created to advance scientific understanding and innovation in magnetic fusion research by enabling more efficient use of existing experimental facilities through more effective integration of experiment, theory, and modeling. To achieve this objective, NFC introduced the concept of "network services", which build on top of computational Grids, and provide Fusion codes, together with their maintenance and hardware resources as a service to the community. This mode of operation requires the development of new authorization and enforcement capabilities. In addition, the nature of Fusion experiments places strident quality of service requirements on codes run during the experimental cycle. In this paper, we describe Grid computing requirements of the Fusion community, and present our first experiments in meeting those requirements.

We present the discovery and timing solutions of five new pulsars by students involved in the Pulsar Search Collaboratory (PSC), a NSF-funded joint program between the National Radio Astronomy Observatory and West Virginia University designed to excite and engage high-school students in Science, Technology, Engineering, and Mathematics (STEM) and related fields. We encourage students to pursue STEM fields by apprenticing them within a professional scientific community doing cutting edge research, specifically by teaching them to search for pulsars. The students are analyzing 300 hours of drift-scan survey data taken with the Green Bank Telescope at 350 MHz. These data cover 2876 square degrees of the sky. Over the course of five years, more than 700 students have inspected diagnostic plots through a web-based graphical interface designed for this project. The five pulsars discovered in the data have spin periods ranging from 3.1 ms to 4.8 s. Among the new discoveries are - PSR J1926-1314, a long period, nulling pulsar; PSR J1821+0155, an isolated, partially recycled 33-ms pulsar; and PSR J1400-1438, a millisecond pulsar in a 9.5-day orbit whose companion is likely a white dwarf star.

The Pulsar Search Collaboratory [PSC, NSF #0737641] is a joint project between the National Radio Astronomy Observatory (NRAO) and West Virginia University (WVU) designed to interest high school students in science, technology, engineering, and mathematics [STEM] related career paths by helping them to conduct authentic scientific research. The 3- year PSC program, which began in summer 2008, teaches students to analyze astronomical radio data acquired with the 100-m Robert C. Byrd Green Bank Telescope for the purpose of discovering new pulsars. We present the results of the first complete year of the PSC, which includes two astronomical discoveries.; Comment: 18 pages, 7 figures

28 pages, 7 figures, 1 table.; The common goal for structural genomic centers and consortiums is to decipher as quickly as possible the three-dimensional structures for a multitude of recombinant proteins derived from known genomic sequences. Since X-ray crystallography is the foremost method to acquire atomic resolution for macromolecules, the limiting step is obtaining protein crystals that can be useful of structure determination. High-throughput methods have been developed in recent years to clone, express, purify, crystallize and determine the three-dimensional structure of a protein gene product rapidly using automated devices, commercialized kits and consolidated protocols. However, the average number of protein structures obtained for most structural genomic groups has been very low compared to the total number of proteins purified. As more entire genomic sequences are obtained for different organisms from the three kingdoms of life, only the proteins that can be crystallized and whose structures can be obtained easily are studied. Consequently, an astonishing number of genomic proteins remain unexamined. In the era of high-throughput processes, traditional methods in molecular biology, protein chemistry and crystallization are eclipsed by automation and pipeline practices. The necessity for high-rate production of protein crystals and structures has prevented the usage of more intellectual strategies and creative approaches in experimental executions. Fundamental principles and personal experiences in protein chemistry and crystallization are minimally exploited only to obtain "low-hanging fruit" protein structures. We review the practical aspects of today's high-throughput manipulations and discuss the challenges in fast pace protein crystallization and tools for crystallography. Structural genomic pipelines can be improved with information gained from low-throughput tactics that may help us reach the higher-bearing fruits. Examples of recent developments in this area are reported from the efforts of the Southeast Collaboratory for Structural Genomics (SECSG).; This report was comprised of investigations supported by the NIGMS Southeast Collaboratory for Structural Genomics...

Este documento se refiere al "Southern Hemisphere Adaptation Collaboratory", una iniciativa de investigación colaborativa entre países del hemisferio sur en materia de adaptación

This paper presents part of the results achieved to date in the process of developing a collaboratory in two R&D organizations. A collaboratory corresponds to a laboratory without walls, in which scientists are connected to each other, to scientific instruments and to information, independently of time and location. These two cases are part of a broader research project engaged in building a collaboratory in order to share knowledge and resources among the Portuguese State Laboratories. The building of the collaboratory is anchored on three main tasks: a) information audits carried out in each of the organizations, in order to map the main information flows, entities, repositories and systems; b) information behaviour research, in order to gain insight into the organizational information culture and the researchers' information use; c) implementation of the appropriate infrastructure and tools, in order to accommodate information archiving and intelligent search, collaborative software, remote control of scientific instruments, and multi-channel access to the services. The case study strategy was adopted because it is particularly amenable to the triangulation of methods (namely document analysis, survey and interviewing) thus providing rich ingredients to characterize a specific context. Discourse analysis was the technique used to analyse the interview transcripts. The research sites are two government R&D institutions operating in the Civil Engineering and in the Nuclear Technology fields...