A Multilaboratory Comparison of Calibration Accuracy and the Performance of External References in Analytical Ultracentrifugation

Analytical ultracentrifugation (AUC) is a first principles based method to determine absolute sedimentation coefficients and buoyant molar masses of macromolecules and their complexes, reporting on their size and shape in free solution. The purpose of this multi-laboratory study was to establish the precision and accuracy of basic data dimensions in AUC and validate previously proposed calibration techniques. Three kits of AUC cell assemblies containing radial and temperature calibration tools and a bovine serum albumin (BSA) reference sample were shared among 67 laboratories, generating 129 comprehensive data sets. These allowed for an assessment of many parameters of instrument performance, including accuracy of the reported scan time after the start of centrifugation, the accuracy of the temperature calibration, and the accuracy of the radial magnification. The range of sedimentation coefficients obtained for BSA monomer in different instruments and using different optical systems was from 3.655 S to 4.949 S, with a mean and standard deviation of (4.304 ± 0.188) S (4.4%). After the combined application of correction factors derived from the external calibration references for elapsed time, scan velocity, temperature, and radial magnification, the range of s-values was reduced 7-fold with a mean of 4.325 S and a 6-fold reduced standard deviation of ± 0.030 S (0.7%). In addition, the large data set provided an opportunity to determine the instrument-to-instrument variation of the absolute radial positions reported in the scan files, the precision of photometric or refractometric signal magnitudes, and the precision of the calculated apparent molar mass of BSA monomer and the fraction of BSA dimers. These results highlight the necessity and effectiveness of independent calibration of basic AUC data dimensions for reliable quantitative studies

A multilaboratory comparison of calibration accuracy and the performance of external references in analytical ultracentrifugation.

Analytical ultracentrifugation (AUC) is a first principles based method to determine absolute sedimentation coefficients and buoyant molar masses of macromolecules and their complexes, reporting on their size and shape in free solution. The purpose of this multi-laboratory study was to establish the precision and accuracy of basic data dimensions in AUC and validate previously proposed calibration techniques. Three kits of AUC cell assemblies containing radial and temperature calibration tools and a bovine serum albumin (BSA) reference sample were shared among 67 laboratories, generating 129 comprehensive data sets. These allowed for an assessment of many parameters of instrument performance, including accuracy of the reported scan time after the start of centrifugation, the accuracy of the temperature calibration, and the accuracy of the radial magnification. The range of sedimentation coefficients obtained for BSA monomer in different instruments and using different optical systems was from 3.655 S to 4.949 S, with a mean and standard deviation of (4.304 ± 0.188) S (4.4%). After the combined application of correction factors derived from the external calibration references for elapsed time, scan velocity, temperature, and radial magnification, the range of s-values was reduced 7-fold with a mean of 4.325 S and a 6-fold reduced standard deviation of ± 0.030 S (0.7%). In addition, the large data set provided an opportunity to determine the instrument-to-instrument variation of the absolute radial positions reported in the scan files, the precision of photometric or refractometric signal magnitudes, and the precision of the calculated apparent molar mass of BSA monomer and the fraction of BSA dimers. These results highlight the necessity and effectiveness of independent calibration of basic AUC data dimensions for reliable quantitative studies

TWiki : A collaborative space of internal documentation, an efficient way to work together

<p>The documentalists at Strasbourg astronomical Data Center treat publications to create content for the SIMBAD and VizieR databases. The publication treatment is quite complex and the ingestion process needs to be described. This requires precise knowledge and mutual support among the documentalists in interaction with computer engineers and astronomers. Documentalists at CDS have thought of an adapted way to organize and enrich their internal documentation. The “TWiki” collaborative space, recently reorganized and enriched, regroups documents about agreed-upon procedures and methods, directions for use of the software and tools, shared problems/solutions. It is a tool for sharing, preserving and enriching the common knowledge of the whole staff.</p

Bibliographical references: From publishers to SIMBAD

The SIMBAD astronomical database hosted by the CDS provides basic data, cross-identifications, bibliography and measurements for astronomical objects outside the solar system. The CDS receives the bibliographic meta-data of the articles published in the main astronomical journals directly from the publishers. How we receive the data and their format vary from one publisher to the next. These data are first extracted and stored in files with a standardised format. Then, to avoid errors or misprints, we perform different tests on these data: - Author names are compared to a reference list maintained at CDS, and the keywords are compared with the AAS list - Astronomical objects are verified by checking their name in the SIMBAD database - A completion test checks that all of articles of a journal volume are present The next step identifies whether an astronomical object appears inside a title, a keyword or an abstract, and if so, we add a link to the object in SIMBAD. Once all of the verifications and corrections have been made we add the meta-data into SIMBAD. We also add other information such as the number of different astronomical objects studied in the paper, the presence tables and their links to VizieR, any new acronyms, as well as some comments. New developments are in progress to automatically extract the data from the tables in the articles (that have not been processed by, or provided to VizieR) . In addition, each night automatic checks are executed to list the new data and to test the coherence of these data in SIMBAD

Bibliographical references: From publishers to SIMBAD

The SIMBAD astronomical database hosted by the CDS provides basic data, cross-identifications, bibliography and measurements for astronomical objects outside the solar system. The CDS receives the bibliographic meta-data of the articles published in the main astronomical journals directly from the publishers. How we receive the data and their format vary from one publisher to the next. These data are first extracted and stored in files with a standardised format. Then, to avoid errors or misprints, we perform different tests on these data: - Author names are compared to a reference list maintained at CDS, and the keywords are compared with the AAS list - Astronomical objects are verified by checking their name in the SIMBAD database - A completion test checks that all of articles of a journal volume are present The next step identifies whether an astronomical object appears inside a title, a keyword or an abstract, and if so, we add a link to the object in SIMBAD. Once all of the verifications and corrections have been made we add the meta-data into SIMBAD. We also add other information such as the number of different astronomical objects studied in the paper, the presence tables and their links to VizieR, any new acronyms, as well as some comments. New developments are in progress to automatically extract the data from the tables in the articles (that have not been processed by, or provided to VizieR) . In addition, each night automatic checks are executed to list the new data and to test the coherence of these data in SIMBAD

TWiki: A Collaborative Space of Internal Documentation, an Efficient Way to Work Together

International audienceThe documentalists at Strasbourg astronomical Data Center (CDS) mine publications in order to update the SIMBAD and VizieR databases with astronomical data. The process of mining publications is quite complex and, over time, the databases and tools used evolve as the field of astronomy evolves. The ingest process needs to be agreed upon, well described, and shared by all involved. This requires specific knowledge and mutual support among the documentalists in interaction with computer engineers and astronomers. The documentalists at CDS have therefore organized and enriched their internal documentation; the wiki collaborative tool is an efficient framework to do so. For more than a decade, the CDS has been developing a "TWiki" collaborative space. Recently, we have created a working group to refurbish the collaborative space and it is now better structured and clearer and this provides new functionality, giving the user a better experience

A New Bibliographical Feature for SIMBAD: Highlighting the Most Relevant Papers for One Astronomical Object

International audienceThe number of bibliographical references attached to an astronomical object in SIMBAD is has been growing continuously over the years. It is important for astronomers to retrieve the most relevant papers, those that give important information about the object of study. This is not easy since there can be many references attached to one object. For instance, in 2014, more than 15,000 objects had been attached to more than 50 references. The location of the object's citations inside the paper and its number of occurrences are important criteria to extract the most relevant papers. Since 2008, because of the DJIN application (a semi-automatic tool to search for object names in full text) this information has been collected. For each article associated with an astronomical object, we know where it is cited and how many times and with which name it appears. Since September 2013, the users of SIMBAD web site can choose to retrieve the most relevant references for an astronomical object depending on its location in the publication. A new formula to sort references by combining all locations, number of occurrences, total number of objects studied, citation count, and year is presented in this paper

How Documentalists Update SIMBAD

International audienceThe Strasbourg astronomical Data Center (CDS) was created in 1972 and has had a major role in astronomy for more than forty years. CDS develops a service called SIMBAD that provides basic data, cross-identifications, bibliography, and measurements for astronomical objects outside the solar system. It brings to the scientific community an added value to content which is updated daily by a team of documentalists working together in close collaboration with astronomers and IT specialists. We explain how the CDS staff updates SIMBAD with object citations in the main astronomical journals, as well as with astronomical data and measurements. We also explain how the identification is made between the objects found in the literature and those already existing in SIMBAD. We show the steps followed by the documentalist team to update the database using different tools developed at CDS, like the sky visualizer Aladin, and the large catalogues and survey database VizieR. As a direct result of this teamwork, SIMBAD integrates almost 10.000 bibliographic references per year. The service receives more than 400.000 queries per day

Working Together at CDS: The Symbiosis Between Astronomers, Documentalists, and IT Specialists

International audienceSince the CDS (Centre de Données astronomiques de Strasbourg) began a little more than forty years ago, astronomers, documentalists, and information technology (IT) specialists have been working together. The synergy between these three professional groups support the core of the work and is becoming more and more crucial with the increasing volume and complexity of data handled. The astronomers use their understanding of the subject and of users' needs to help to maintain the accuracy and the relevance of data. The computer engineers enhance these data by maintaining the database framework and continuing to add useful tools to retrieve and reuse this content. Finally, the documentalists, by definition, manage the content. They do so with the help of IT tools developed at CDS; they analyze the publications, extract the relevant information, verify the data, make comparisons with existing data, add the useful information in VizieR and SIMBAD, and confer with astronomers to make corrections, if needed. After an historical review of the evolution in data and the way data have been provided at CDS, we will further discuss the fundamental roles of the three professional groups to support the mission of the CDS