Science for Environment Policy features a policy brief explaining the biases around biodiversity databases in their latest issue 331, from 6 June 2013. "Biodiversity databases: language and location help explain biases" features a new study arguing that low numbers of English speakers, large distances from the database host and low security acting as key barriers to data collection and among the main reasons for the underrepresentation of some countries in biodiversity databases.

Source: Amano T., Sutherland W.J. (2013) Four barriers to the global understanding of biodiversity conservation: wealth, language, geographical location and security. Proceedings of the Royal Society B. 280: 20122649. doi: 10.1098/rspb.2012.2649

The German working group on vegetation databases is dedicated to building, maintaining, linking and analysing electronic archives of vegetation plot data and provides the national repository "VegetWeb", hosted by the German Federal Agency for Nature Conservation (BfN). The 12th workshop will be hosted by the new German Centre for Integrative Biodiversity Research (iDiv) in Leipzig, Germany. The central mission of iDiv is to promote theory-driven experiments and synthesis as well as data-driven theory. The concept of iDiv encompasses the detection of biodiversity, understanding its emergence, exploring its consequences for ecosystem functions and services, and developing strategies to safeguard biodiversity under global change. In this context, the combined synthesis of species abundance and distribution data together with information on species characteristics is seen as a high potential to advance our understanding of community assembly and plant diversity patterns. For this reason, important databases have already become part of iDiv's data research platforms, such as the German Vegetation Reference Database (GVRD), the plant trait databases TRY and BIOLFLOR and the Chorology Database Halle (CDH) on plant distribution data. In this workshop, we seek to explore the potentials of such databases for future research, with a specific focus on vegetation databases.
Further Information: http://www.botanik.uni-greifswald.de/idiv_meeting_2013.html

Interoperability of crystallographic data with other disciplines is essential for the smooth and rapid progress of structure-based science in the computer age. Within crystallography and closely related subject areas, there is already a high level of conformance to the generally accepted FAIR principles (that data be findable, accessible, interoperable and reusable) through the adoption of common information exchange protocols by databases, publishers, instrument vendors, experimental facilities and software authors. Driven by the success within these domains, the IUCr has worked closely with CODATA (the Committee on Data of the International Science Council) to help develop the latter's commitment to cross-domain integration of discipline-specific data. The IUCr has, in particular, emphasized the need for standards relating to data quality and completeness as an adjunct to the FAIR data landscape. This can ensure definitive reusable data, which in turn can aid interoperability across domains. A microsymposium at the IUCr 2023 Congress provided an up-to-date survey of data interoperability within and outside of crystallography, expounded using a broad range of examples.

This article presents a web-based framework to build a database without in-depth programming knowledge given a set of CIF dictionaries and a collection of CIFs. The framework consists of two main elements: the public site that displays the information contained in the CIFs in an ordered manner, and the restricted administrative site which defines how that information is stored, processed and, eventually, displayed. Thus, the web application allows users to easily explore, filter and access the data, download the original CIFs, and visualize the structures via JSmol. The modulated structures open database B-IncStrDB, the official International Union of Crystallography repository for this type of material and available through the Bilbao Crystallographic Server, has been re-implemented following the proposed framework.

In this espisode we take a closer look at relational database systems and the concepts behind them. We start by discussing the relational paradigm, its concepts and ramifications, and go on to architectural aspects.

Recording Venue: Skype Guest: Michael Hunger Michael Hunger of Neo Technology, and a developer on the Neo4J database, joins Robert to discuss graph databases. Graph databases fall within the larger category of NoSQL databases but they are not primarily a solution to problems of scale. They differentiate themselves from RDBMS in offering a data model built […]

Recording Venue: Skype Guest: Michael Stonebraker Dr. Michael Stonebraker, one of the leading researchers and technology entrepreneurs in the database space, joins Robert for a discussion of database architecture and the emerging NewSQL family of databases. Dr. Stonebraker opens with his take on how the database market is segmented around a small number of use […]

Max Neunhoffer of ArangoDB discusses about multi-model databases in general, and open source ArangoDB, in specific, with show host Nishant Suneja. The show discussion covers motivation behind deploying a multi-model database in an enterprise setting, and deep dives into ArangoDB internals.

Audrey Lawrence of Amazon discusses Timeseries Databases and their new database offering Amazon Timestream. Philip Winston spoke with Lawrence about data modeling, ingestion, queries, performance, life-cycle management, hot data vs. cold data...

Yingjun Wu, founder of RisingWave Labs and previously a software engineer at Amazon Web Services and researcher at IBM Almaden Research Center, speaks with SE Radio host Brijesh Ammanath about streaming databases. After considering the benefits and unique challenges, they delve into the architecture and design patterns of streaming databases, as well as the evolution and security considerations. Yingjun also talks about the future of streaming databases, including the potential impact that Amazon S3 Express One Zone will have on the streaming landscape, and how the unified batch and streaming might evolve in the database world. Brought to you by IEEE Computer Society and IEEE Software magazine.

How important is the DX of software vs how important is the person showing off the software, Douglas Crockford and JSON, remembering XML, trying to write better HTML for email, new TC39 proposal, workshopping t-shirts, and what do you do if you want a little bit of database on your website?

Are you using MySQL’s utf8 charset in your databases? In this write-up I’ll explain why you should switch to utf8mb4 instead, and how to do it.

Earth scientists plan to meld massive databases into a 'geological Google'  Science Magazine

CsCl-type materials have many outstanding characteristics, i.e. simple in structure, ease of synthesis and good stability at room temperature, thus are an excellent choice for designing functional materials. Using high-throughput first-principles calculations, a large number of topological semimetals/metals (TMs) were designed from CsCl-type materials found in crystallographic databases and their crystal and electronic structures have been studied. The CsCl-type TMs in this work show rich topological character, ranging from triple nodal points, type-I nodal lines and critical-type nodal lines, to hybrid nodal lines. The TMs identified show clean topological band structures near the Fermi level, which are suitable for experimental investigations and future applications. This work provides a rich data set of TMs with a CsCl-type structure.

Molecular replacement (MR) is the predominant route to solution of the phase problem in macromolecular crystallography. Where the lack of a suitable homologue precludes conventional MR, one option is to predict the target structure using bioinformatics. Such modelling, in the absence of homologous templates, is called ab initio or de novo modelling. Recently, the accuracy of such models has improved significantly as a result of the availability, in many cases, of residue-contact predictions derived from evolutionary covariance analysis. Covariance-assisted ab initio models representing structurally uncharacterized Pfam families are now available on a large scale in databases, potentially representing a valuable and easily accessible supplement to the PDB as a source of search models. Here, the unconventional MR pipeline AMPLE is employed to explore the value of structure predictions in the GREMLIN and PconsFam databases. It was tested whether these deposited predictions, processed in various ways, could solve the structures of PDB entries that were subsequently deposited. The results were encouraging: nine of 27 GREMLIN cases were solved, covering target lengths of 109–355 residues and a resolution range of 1.4–2.9 Å, and with target–model shared sequence identity as low as 20%. The cluster-and-truncate approach in AMPLE proved to be essential for most successes. For the overall lower quality structure predictions in the PconsFam database, remodelling with Rosetta within the AMPLE pipeline proved to be the best approach, generating ensemble search models from single-structure deposits. Finally, it is shown that the AMPLE-obtained search models deriving from GREMLIN deposits are of sufficiently high quality to be selected by the sequence-independent MR pipeline SIMBAD. Overall, the results help to point the way towards the optimal use of the expanding databases of ab initio structure predictions.

Identifying emerging research areas and technologies is important for decision makers, but notoriously difficult to do. This study presents a new way of searching the literature to identify emerging topics, which will help policymakers, industry and funding bodies to make better decisions.

Richer countries have more resources for gathering biodiversity information, creating a biased view of the worlds' species and their distribution. However, a new study argues that there are other reasons why some countries are underrepresented in global biodiversity databases, with low numbers of English speakers, large distances from the database host and low security acting as key barriers to data collection.

oscon: RT @OReillyMedia #Video Deal/Week: Data and Databases at #OSCON 2012 - $49.99 (Save 50%) Use code VDWK http://t.co/BnDD750NQv

strataconf: The Future Is Graph Databases http://t.co/BVxOZwtoKS A Conversation with @EmilEifrem, founder of @Neo4J #strataconf

I'm in the process of weeding a regression test list. I have a coverage database from the full regression list and would like to diff it with the coverage database from the new reduced regression test list. If possible I would than like to trace back any buckets covered with the full list, but not with the partial list, into the original tests that covered them.

Is that possible using IMC? if not, is it possible to do from Specman itself?

(Note that we're not using vManager)

Thanks,

Avidan

BIOVIA Direct

The country’s two biggest tobacco companies have agreed to improve public access to internal tobacco-industry documents and to pay $6.25 million into a court fund that will go to support the country’s largest online collection of tobacco documents.

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Jukic, Nenad, author

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03:45 What makes the Gun database engine special

07:00 Defining a database

12:58 The CAP Theorem

22:56 What Graphs are and how they function (circular references)

30:32 Gun and rotational disk systems

32:08 Gun’s optimizations for performance in ensuing versions

39:55 The prevalence of open source companies

42:45 Further discussing the CAP Theorem and its nuances

50:33 Gun’s purpose and design

52:13 What a Firebase is

54:22 How to get started with Gun - Visit Gun Tutorial,  Gun's Github Page, and

Gun Node Module

QUOTES:

“I think the database should bend to your application’s demands, rather than you having to bend to the database’s demands.” –Mark Nadal

“…The protocol that GUN defines is something that can be implemented in any language. Because GUN is in the language, you don’t have the context which latency of having to make an HTTP call or socket request…” –AJ O’Neill

“Let’s demystify the black magic of CAP.” –Mark Nadal

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