scholarly journals MultiCellDS: a community-developed standard for curating microenvironment-dependent multicellular data

2016 ◽  
Author(s):  
Samuel H. Friedman ◽  
Alexander R. A. Anderson ◽  
David M. Bortz ◽  
Alexander G. Fletcher ◽  
Hermann B. Frieboes ◽  
...  

AbstractExchanging and understanding scientific data and their context represents a significant barrier to advancing research, especially with respect to information siloing. Maintaining information provenance and providing data curation and quality control help overcome common concerns and barriers to the effective sharing of scientific data. To address these problems in and the unique challenges of multicellular systems, we assembled a panel composed of investigators from several disciplines to create the MultiCellular Data Standard (MultiCellDS) with a use-case driven development process. The standard includes (1) digital cell lines, which are analogous to traditional biological cell lines, to record metadata, cellular microenvironment, and cellular phenotype variables of a biological cell line, (2) digital snapshots to consistently record simulation, experimental, and clinical data for multicellular systems, and (3) collections that can logically group digital cell lines and snapshots. We have created a MultiCellular DataBase (MultiCellDB) to store digital snapshots and the 200+ digital cell lines we have generated. MultiCellDS, by having a fixed standard, enables discoverability, extensibility, maintainability, searchability, and sustainability of data, creating biological applicability and clinical utility that permits us to identify upcoming challenges to uplift biology and strategies and therapies for improving human health.

2008 ◽  
Vol 2 (2) ◽  
pp. 111-121
Author(s):  
Ragini Raj Singh ◽  
◽  
Amit Ron ◽  
Nick Fishelson ◽  
Irena Shur ◽  
...  

Dielectric spectroscopy (DS) of living biological cells is based on the analysis of cells suspended in a physiological medium. It provides knowledge of the polarization-relaxation response of the cells to external electric field as function of the excitation frequency. This response is strongly affected by both structural and molecular properties of the cells and, therefore, can reveal rare insights into cell physiology and behaviour. This study demonstrates the mapping potential of DS after cytoplasmic and membranal markers for cell-based screening analysis. The effect of membrane permittivity and cytoplasm conductivity was examined using tagged MBA and MDCK cell lines respectively. The comparison of the dielectric spectra of tagged and native cell lines reveals clear differences between the cells. In addition, the differences in the matching dielectric properties of the cells were discovered. Those findings support the high distinction resolution and sensitivity of DS after fine molecular and cellular changes, and hence, highlight the high potential of DS as non invasive screening tool in cell biology research.


Author(s):  
Matt Woodburn ◽  
Gabriele Droege ◽  
Sharon Grant ◽  
Quentin Groom ◽  
Janeen Jones ◽  
...  

The utopian vision is of a future where a digital representation of each object in our collections is accessible through the internet and sustainably linked to other digital resources. This is a long term goal however, and in the meantime there is an urgent need to share data about our collections at a higher level with a range of stakeholders (Woodburn et al. 2020). To sustainably achieve this, and to aggregate this information across all natural science collections, the data need to be standardised (Johnston and Robinson 2002). To this end, the Biodiversity Information Standards (TDWG) Collection Descriptions (CD) Interest Group has developed a data standard for describing collections, which is approaching formal review for ratification as a new TDWG standard. It proposes 20 classes (Suppl. material 1) and over 100 properties that can be used to describe, categorise, quantify, link and track digital representations of natural science collections, from high-level approximations to detailed breakdowns depending on the purpose of a particular implementation. The wide range of use cases identified for representing collection description data means that a flexible approach to the standard and the underlying modelling concepts is essential. These are centered around the ‘ObjectGroup’ (Fig. 1), a class that may represent any group (of any size) of physical collection objects, which have one or more common characteristics. This generic definition of the ‘collection’ in ‘collection descriptions’ is an important factor in making the standard flexible enough to support the breadth of use cases. For any use case or implementation, only a subset of classes and properties within the standard are likely to be relevant. In some cases, this subset may have little overlap with those selected for other use cases. This additional need for flexibility means that very few classes and properties, representing the core concepts, are proposed to be mandatory. Metrics, facts and narratives are represented in a normalised structure using an extended MeasurementOrFact class, so that these can be user-defined rather than constrained to a set identified by the standard. Finally, rather than a rigid underlying data model as part of the normative standard, documentation will be developed to provide guidance on how the classes in the standard may be related and quantified according to relational, dimensional and graph-like models. So, in summary, the standard has, by design, been made flexible enough to be used in a number of different ways. The corresponding risk is that it could be used in ways that may not deliver what is needed in terms of outputs, manageability and interoperability with other resources of collection-level or object-level data. To mitigate this, it is key for any new implementer of the standard to establish how it should be used in that particular instance, and define any necessary constraints within the wider scope of the standard and model. This is the concept of the ‘collection description scheme,’ a profile that defines elements such as: which classes and properties should be included, which should be mandatory, and which should be repeatable; which controlled vocabularies and hierarchies should be used to make the data interoperable; how the collections should be broken down into individual ObjectGroups and interlinked, and how the various classes should be related to each other. which classes and properties should be included, which should be mandatory, and which should be repeatable; which controlled vocabularies and hierarchies should be used to make the data interoperable; how the collections should be broken down into individual ObjectGroups and interlinked, and how the various classes should be related to each other. Various factors might influence these decisions, including the types of information that are relevant to the use case, whether quantitative metrics need to be captured and aggregated across collection descriptions, and how many resources can be dedicated to amassing and maintaining the data. This process has particular relevance to the Distributed System of Scientific Collections (DiSSCo) consortium, the design of which incorporates use cases for storing, interlinking and reporting on the collections of its member institutions. These include helping users of the European Loans and Visits System (ELViS) (Islam 2020) to discover specimens for physical and digital loans by providing descriptions and breakdowns of the collections of holding institutions, and monitoring digitisation progress across European collections through a dynamic Collections Digitisation Dashboard. In addition, DiSSCo will be part of a global collections data ecosystem requiring interoperation with other infrastructures such as the GBIF (Global Biodiversity Information Facility) Registry of Scientific Collections, the CETAF (Consortium of European Taxonomic Facilities) Registry of Collections and Index Herbariorum. In this presentation, we will introduce the draft standard and discuss the process of defining new collection description schemes using the standard and data model, and focus on DiSSCo requirements as examples of real-world collection descriptions use cases.


2017 ◽  
Vol 9 (3) ◽  
pp. 34-53 ◽  
Author(s):  
Ignacio Alvarez ◽  
Laura Rumbel

This paper describes the research and development process of an in-vehicle user experience using Skyline, an automotive prototyping platform created in Intel Labs to empower interaction designers and user experience researches to rapidly and iteratively develop and test in-vehicle user experience concepts. The paper describes the hardware and software components of Skyline in depth and how to configure them to suit individual researcher needs. The paper also presents a case study to exemplify the design making process that Skyline enables. From ideation to use-case creation, prototyping and validation through user assessment, the paper showcases the benefits of capturing early qualitative user feedback as support for rapid prototyping walking through a study titled Agency vs. Control and the associated interactions inside the cockpit. Ten defined use-cases are developed and integrated into a hero scenario in Skyline. High fidelity HMI concepts are tested and validated over the course of six months with feedback from a total of fifty users.


1993 ◽  
Vol 1 (3) ◽  
pp. 213-233 ◽  
Author(s):  
Frédéric Gruau ◽  
Darrell Whitley

A grammar tree is used to encode a cellular developmental process that can generate whole families of Boolean neural networks for computing parity and symmetry. The development process resembles biological cell division. A genetic algorithm is used to find a grammar tree that yields both architecture and weights specifying a particular neural network for solving specific Boolean functions. The current study particularly focuses on the addition of learning to the development process and the evolution of grammar trees. Three ways of adding learning to the development process are explored. Two of these exploit the Baldwin effect by changing the fitness landscape without using Lamarckian evolution. The third strategy is Lamarckian in nature. Results for these three modes of combining learning with genetic search are compared against genetic search without learning. Our results suggest that merely using learning to change the fitness landscape can be as effective as Lamarckian strategies at improving search.


2020 ◽  
Vol 25 (6) ◽  
pp. 5333-5369 ◽  
Author(s):  
Steffen Herbold ◽  
Alexander Trautsch ◽  
Fabian Trautsch

Abstract Context Issue tracking systems are used to track and describe tasks in the development process, e.g., requested feature improvements or reported bugs. However, past research has shown that the reported issue types often do not match the description of the issue. Objective We want to understand the overall maturity of the state of the art of issue type prediction with the goal to predict if issues are bugs and evaluate if we can improve existing models by incorporating manually specified knowledge about issues. Method We train different models for the title and description of the issue to account for the difference in structure between these fields, e.g., the length. Moreover, we manually detect issues whose description contains a null pointer exception, as these are strong indicators that issues are bugs. Results Our approach performs best overall, but not significantly different from an approach from the literature based on the fastText classifier from Facebook AI Research. The small improvements in prediction performance are due to structural information about the issues we used. We found that using information about the content of issues in form of null pointer exceptions is not useful. We demonstrate the usefulness of issue type prediction through the example of labelling bugfixing commits. Conclusions Issue type prediction can be a useful tool if the use case allows either for a certain amount of missed bug reports or the prediction of too many issues as bug is acceptable.


2015 ◽  
Vol 48 (1) ◽  
pp. 301-305 ◽  
Author(s):  
Mark Könnecke ◽  
Frederick A. Akeroyd ◽  
Herbert J. Bernstein ◽  
Aaron S. Brewster ◽  
Stuart I. Campbell ◽  
...  

NeXus is an effort by an international group of scientists to define a common data exchange and archival format for neutron, X-ray and muon experiments. NeXus is built on top of the scientific data format HDF5 and adds domain-specific rules for organizing data within HDF5 files, in addition to a dictionary of well defined domain-specific field names. The NeXus data format has two purposes. First, it defines a format that can serve as a container for all relevant data associated with a beamline. This is a very important use case. Second, it defines standards in the form of application definitions for the exchange of data between applications. NeXus provides structures for raw experimental data as well as for processed data.


Author(s):  
Patavee Charnvivit ◽  
Nuttakorn Thubthong ◽  
Sudaporn Luksaneeyanawin

Software testing is an important activity in software development process. Testers have to generate test cases to test a system. At least, test cases consist of test input values and expected results. In functional testing or black-box testing, test designers can generate test cases from a requirements specification document which includes diagrams such as UML Diagrams. In this research, we consider UML use case diagrams and propose an approach for generating test cases from use cases based on a limited entries decision table. These test cases cover all success and alternative scenarios in a use case as well as all events that contain include and extend relationship.


2016 ◽  
Vol 9 (1) ◽  
Author(s):  
Andri Kulung ◽  
Steven Sentinuwo ◽  
Alicia Sinsuw

Bahasa Mandarin merupakan salah satu Bahasa yang terkenal di seluruh dunia. Ada sekitar 1.302 juta orang dengan berbagai kalangan umur telah menggunakan Bahasa mandarin, sehingga karena alasan tersebut banyak sekolah termasuk Sekolah Dasar (SD) Advent 1 Tikala Manado telah memasukkan Bahasa Mandarin sebagai salah satu mata pelajaran Bahasa asing. Namun siswa-siswa SD Advent 1 Tikala Manado merasa kesulitan dalam mempelajari Bahasa Mandarin dikarenakan tidak adanya media pembelajaran yang dapat membantu mereka dalam mempelajari Bahasa Mandarin di luar jam sekolah. Aplikasi pembelajaran Bahasa Mandarin Dasar merupakan solusi untuk membantu siswa SD Advent 1 Tikala Manado dalam mempelajari Bahasa Mandarin, baik dalam proses pembelajaran di sekolah maupun di luar sekolah. Unified Software Development Process (USDP) merupakan metode pengembangan perangkat lunak yang prosesnya dikendalikan oleh Use Case (use case driven) dan dikerjakan secara berulang (iterative) sehingga pada akhirnya menghasilkan perangkat lunak terintegrasi berukuran besar yang terbentuk secara bertahap (Incremental) dengan bantuan Unified Modeling Language (UML) sebagai alat bantu utama analisis dan perancangan sistem perangkat lunak. Aplikasi pembelajaran Bahasa Mandarin Dasar dibuat dengan fitur belajar dan bermain. Fitur belajar dilengkapi dengan materi pengajaran yang digolongkan ke dalam  beberapa kategori yaitu kategori kelas 1, kelas 2, dan kelas 3 serta sub fitur berupa suara dengan tujuan siswa bisa mengetahui cara pengucapan suatu kata. Dengan dibuatnya aplikasi ini diharapkan agar aplikasi ini bisa membantu siswa dalam mempelajari Bahasa Mandarin pada jam sekolah maupun diluar jam sekolah.


Author(s):  
K Usha S Pai ◽  
Yadav D. Bodke ◽  
M Manjunath Setty ◽  
Savaliya Mihir ◽  
Keerthi Priya ◽  
...  

Cancer is one of the major causes of death in the world today. Although chemotherapeutic regimen remains the prime treatment of cancer, it is important to explore for newer compounds due to their adverse reactions and the growing rate of resistance. Traditionally, some plants are used for the treatment of cancers in India. However, no scientific data backing the evidence exists for the same. Among such plants is Cleome viscosa Linn, which is used in the Indian system of medicine for cancer treatment. To test its anticancer activity and generate scientifically reliable data, the extraction of whole plant has been carried out using methanol and fractions were generated using petroleum ether, dichloromethane, ethyl acetate and n-butanol. The fractions were first tested in vitro for their antiproliferative activity and mechanistic studies. In this paper, we report the anticancer potential of the fractions by a preliminary cytotoxicity activity in vitro using cell lines followed by the liquid tumor (EAC) model in mice. Upon screening on a panel of cancer cell lines, the fractions of petroleum ether, dichloromethane and ethyl acetate were found to possess significant cytotoxic activity on Hela and U343 cell lines. With this evidence, we have then tested the in vivo activity on mice using the liquid tumor model in which the fractions of pet ether, dichloromethane and ethyl acetate exhibit a potential anticancer activity which is evident in characteristics like inhibition of tumor progression, increase in the mean survival time and percentage increased life span along with a decrease in tumor volume. The fractions also showed significant anti-oxidant properties.


2021 ◽  
Vol 11 (14) ◽  
pp. 6464
Author(s):  
Tomas Skersys ◽  
Paulius Danenas ◽  
Rimantas Butleris ◽  
Armantas Ostreika ◽  
Jonas Ceponis

In the domain of model-driven system engineering, model-to-model (M2M) transformations present a very relevant topic because they may provide much-needed automation capabilities to the whole CASE-supported system development life cycle. Nonetheless, it is observed that throughout the whole development process M2M transformations are spread unevenly; in this respect, the phases of Business Modeling and System Analysis are arguably the most underdeveloped ones. The main novelty and contributions of this paper are the presented set of model-based transformations for extracting well-structured SBVR business vocabularies from visual UML use case models, which utilizes M2M transformation technology based on the so-called drag-and-drop actions. The conducted experiments show that this new development provides the same transformation power while introducing more flexibility to the model development process as compared to our previously developed approach for (semi-)automatic extraction of SBVR business vocabularies from UML use case models.


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