Martin Fritts

ISA-TAB-Nano: A Specification for Sharing Nanomaterial Research Data in Spreadsheet-based Format

Background and motivationThe high-throughput genomics communities have been successfully using standardized spreadsheet-based formats to capture and share data within labs and among public repositories. The nanomedicine community has yet to adopt similar standards to share the diverse and multi-dimensional types of data (including metadata) pertaining to the description and characterization of nanomaterials. Owing to the lack of standardization in representing and sharing nanomaterial data, most of the data currently shared via publications and data resources are incomplete, poorly-integrated, and not suitable for meaningful interpretation and re-use of the data. Specifically, in its current state, data cannot be effectively utilized for the development of predictive models that will inform the rational design of nanomaterials.ResultsWe have developed a specification called ISA-TAB-Nano, which comprises four spreadsheet-based file formats for representing and integrating various types of nanomaterial data. Three file formats (Investigation, Study, and Assay files) have been adapted from the established ISA-TAB specification; while the Material file format was developed de novo to more readily describe the complexity of nanomaterials and associated small molecules. In this paper, we have discussed the main features of each file format and how to use them for sharing nanomaterial descriptions and assay metadata.ConclusionThe ISA-TAB-Nano file formats provide a general and flexible framework to record and integrate nanomaterial descriptions, assay data (metadata and endpoint measurements) and protocol information. Like ISA-TAB, ISA-TAB-Nano supports the use of ontology terms to promote standardized descriptions and to facilitate search and integration of the data. The ISA-TAB-Nano specification has been submitted as an ASTM work item to obtain community feedback and to provide a nanotechnology data-sharing standard for public development and adoption.

Nanoinformatics and DNA-based computing: catalyzing nanomedicine.

Five decades of research and practical application of computers in biomedicine has given rise to the discipline of medical informatics, which has made many advances in genomic and translational medicine possible. Developments in nanotechnology are opening up the prospects for nanomedicine and regenerative medicine where informatics and DNA computing can become the catalysts enabling health care applications at sub-molecular or atomic scales. Although nanomedicine promises a new exciting frontier for clinical practice and biomedical research, issues involving cost-effectiveness studies, clinical trials and toxicity assays, drug delivery methods, and the implementation of new personalized therapies still remain challenging. Nanoinformatics can accelerate the introduction of nano-related research and applications into clinical practice, leading to an area that could be called “translational nanoinformatics.” At the same time, DNA and RNA computing presents an entirely novel paradigm for computation. Nanoinformatics and DNA-based computing are together likely to completely change the way we model and process information in biomedicine and impact the emerging field of nanomedicine most strongly. In this article, we review work in nanoinformatics and DNA (and RNA)-based computing, including applications in nanopediatrics. We analyze their scientific foundations, current research and projects, envisioned applications and potential problems that might arise from them.

Informatics and Standards for Nanomedicine Technology

There are several issues to be addressed concerning the management and effective use of information (or data), generated from nanotechnology studies in biomedical research and medicine. These data are large in volume, diverse in content, and are beset with gaps and ambiguities in the description and characterization of nanomaterials. In this work, we have reviewed three areas of nanomedicine informatics: information resources; taxonomies, controlled vocabularies, and ontologies; and information standards. Informatics methods and standards in each of these areas are critical for enabling collaboration; data sharing; unambiguous representation and interpretation of data; semantic (meaningful) search and integration of data; and for ensuring data quality, reliability, and reproducibility. In particular, we have considered four types of information standards in this article, which are standard characterization protocols, common terminology standards, minimum information standards, and standard data communication (exchange) formats. Currently, because of gaps and ambiguities in the data, it is also difficult to apply computational methods and machine learning techniques to analyze, interpret, and recognize patterns in data that are high dimensional in nature, and also to relate variations in nanomaterial properties to variations in their chemical composition, synthesis, characterization protocols, and so on. Progress toward resolving the issues of information management in nanomedicine using informatics methods and standards discussed in this article will be essential to the rapidly growing field of nanomedicine informatics.

Nanoinformatics: a new area of research in nanomedicine

Over a decade ago, nanotechnologists began research on applications of nanomaterials for medicine. This research has revealed a wide range of different challenges, as well as many opportunities. Some of these challenges are strongly related to informatics issues, dealing, for instance, with the management and integration of heterogeneous information, defining nomenclatures, taxonomies and classifications for various types of nanomaterials, and research on new modeling and simulation techniques for nanoparticles. Nanoinformatics has recently emerged in the USA and Europe to address these issues. In this paper, we present a review of nanoinformatics, describing its origins, the problems it addresses, areas of interest, and examples of current research initiatives and informatics resources. We suggest that nanoinformatics could accelerate research and development in nanomedicine, as has occurred in the past in other fields. For instance, biomedical informatics served as a fundamental catalyst for the Human Genome Project, and other genomic and –omics projects, as well as the translational efforts that link resulting molecular-level research to clinical problems and findings.

Nanoinformatics: developing new computing applications for nanomedicine

Nanoinformatics has recently emerged to address the need of computing applications at the nano level. In this regard, the authors have participated in various initiatives to identify its concepts, foundations and challenges. While nanomaterials open up the possibility for developing new devices in many industrial and scientific areas, they also offer breakthrough perspectives for the prevention, diagnosis and treatment of diseases. In this paper, we analyze the different aspects of nanoinformatics and suggest five research topics to help catalyze new research and development in the area, particularly focused on nanomedicine. We also encompass the use of informatics to further the biological and clinical applications of basic research in nanoscience and nanotechnology, and the related concept of an extended “nanotype” to coalesce information related to nanoparticles. We suggest how nanoinformatics could accelerate developments in nanomedicine, similarly to what happened with the Human Genome and other -omics projects, on issues like exchanging modeling and simulation methods and tools, linking toxicity information to clinical and personal databases or developing new approaches for scientific ontologies, among many others.

In-Silico Nanobio-Design. A New Frontier in Computational Biology

Nanobiology is a fast-emerging discipline that brings the tools of nanotechnology to the biological sciences. The introduction of new techniques may accelerate the development of highly specific biomedical treatments, increase their efficiency, and minimize their side effects. Introducing foreign bodies into the complex machinery of the human body is, however, a great and humbling challenge, as past experience has shown. In order for nanobiology to reach its full potential, we must devise a means to alter the properties of nanoparticles, as expressed in the human body, in a predictable manner. Computer-aided methods are the natural option to speed up the development of these technologies. Yet, the procedures for annotation and simulation of nanoparticle properties must be developed and their limitations understood before computational methods can be fully exploited. In this review we will compare the state of development of nanoscale simulations in the biological sciences to that of the computer-aided drug design efforts in the past, tracing a historical parallel between both disciplines. From this comparison, lessons can be learned and bottlenecks identified, helping to speed up the development of computer-aided nanobiodevice design tools.

Adaptive gridding strategies for Free-Lagrangian calculations of low speed flows

Abstract Free-Lagrangian methods have been employed in two-dimensional simulations of the long-term evolution of fluid instabilities for low speed flows. For example, calculations of the Rayleigh-Taylor instability have proceeded through the inversion and mixing of two fluid layers and simulations of droplet deformations have continued well beyond droplet shattering. The freedom to choose grid connections permits several important benefits for these calculations. 1. 1. Mass conservation is enforced for all individual fluid elements. 2. 2. Vertex movement is always Lagrangian. 3. 3. Grid adjustments can be made automatically, with no user intervention. 4. 4. Grid connections may be selected to ensure accuracy in the difference equations. 5. 5. Adaptive gridding schemes are local, adding and deleting vertices as dictated by local accuracy estimators. 6. 6. Any geometric configuration may be easily gridded, for any vertex distribution on the boundaries or in the interior of the fluids. This paper will review some two-dimensional results, with the emphasis on the adaptive gridding algorithms and the accuracy of the resultant difference templates for the mathematical operators. The relation of the triangular mesh to the Voronoi mesh will be explored, particularly for the case when they are dual meshes. Three-dimensional algorithms for adaptive gridding will be presented which are exact analogues to the two-dimensional case. Gridding efficiencies will be discussed for several schemes.

Technology and design for stars & stripes

Abstract The 4 February 1987 victory of STARS & STRIPES in the Americas Cup races off Perth, Western Australia, was a culmination of a three-year project of broad scope and great intensity. The design/technology team approach used to develop the 12-meter yacht STARS & STRIPES is presented. This is, by far, the most comprehensive design/technology effort in the history of yacht design. The effort includes three separate yacht-design firms, advanced computational tools, forty 1/3 scale model tests and a very sophisticated full-scale yacht evaluation procedure. The total performance evaluation system, which integrates the myriad details of yacht designs and race tactics with the flow-code results into a single figure of merit, the relative speed of 12-meter yachts around the race course, is discussed. The SAIC team has been responsible for the major part of the technology development and implementation as well as the coordination of the total technology effort which has resulted in the design and building of four new 12-meter yachts, all of which are named STARS & STRIPES. Also discussed is how the STARS & STRIPES design/technology team was able to successfully modify the winglet-keel design in December prior to the final races.

Integration among databases and data sets to support productive nanotechnology: Challenges and recommendations

Many groups within the broad field of nanoinformatics are already developing data repositories and analytical tools driven by their individual organizational goals. Integrating these data resources across disciplines and with non-nanotechnology resources can support multiple objectives by enabling the reuse of the same information. Integration can also serve as the impetus for novel scientific discoveries by providing the framework to support deeper data analyses. This article discusses current data integration practices in nanoinformatics and in comparable mature fields, and nanotechnology-specific challenges impacting data integration. Based on results from a nanoinformatics-community-wide survey, recommendations for achieving integration of existing operational nanotechnology resources are presented. Nanotechnology-specific data integration challenges, if effectively resolved, can foster the application and validation of nanotechnology within and across disciplines. This paper is one of a series of articles by the Nanomaterial Data Curation Initiative that address data issues such as data curation workflows, data completeness and quality, curator responsibilities, and metadata.

Design systems for adaptive general connectivity meshes: Increasing total efficiency for computational physics applications

To be used effectively in a design environment, numerical tools must accommodate very practical constraints, particularly time deadlines, the need to address multiple design goals and the requirement to minimize risk. This paper advocates the accelerated development of design systems to augment the use of computational physics and to help designers achieve greater efficiency and scope. The role of numerical codes employing general connectivity meshes is stressed. Examples are taken from a design system which is currently being developed for use with tetrahedral volume grids and triangular surface meshes.