LAS: a software platform to support oncological data management

The rapid technological evolution in the biomedical and molecular oncology fields is providing research laboratories with huge amounts of complex and heterogeneous data. Automated systems are needed to manage and analyze this knowledge, allowing the discovery of new information related to tumors and the improvement of medical treatments. This paper presents the Laboratory Assistant Suite (LAS), a software platform with a modular architecture designed to assist researchers throughout diverse laboratory activities. The LAS supports the management and the integration of heterogeneous biomedical data, and provides graphical tools to build complex analyses on integrated data. Furthermore, the LAS interfaces are designed to ease data collection and management even in hostile environments (e.g., in sterile conditions), so as to improve data qualit

Benchmarking SciDB Data Import on HPC Systems

SciDB is a scalable, computational database management system that uses an array model for data storage. The array data model of SciDB makes it ideally suited for storing and managing large amounts of imaging data. SciDB is designed to support advanced analytics in database, thus reducing the need for extracting data for analysis. It is designed to be massively parallel and can run on commodity hardware in a high performance computing (HPC) environment. In this paper, we present the performance of SciDB using simulated image data. The Dynamic Distributed Dimensional Data Model (D4M) software is used to implement the benchmark on a cluster running the MIT SuperCloud software stack. A peak performance of 2.2M database inserts per second was achieved on a single node of this system. We also show that SciDB and the D4M toolbox provide more efficient ways to access random sub-volumes of massive datasets compared to the traditional approaches of reading volumetric data from individual files. This work describes the D4M and SciDB tools we developed and presents the initial performance results. This performance was achieved by using parallel inserts, a in-database merging of arrays as well as supercomputing techniques, such as distributed arrays and single-program-multiple-data programming.Comment: 5 pages, 4 figures, IEEE High Performance Extreme Computing (HPEC) 2016, best paper finalis

Designing interoperable museum information systems

Museum collections are characterized by heterogeneity, since they usually host a plethora of objects of categories, while each of them requires different description policies and metadata standards. Moreover the museum records, which keep the history and evolution of the hosted collections, request proactive curation in order to preserve this rich and diverse information. In this paper, the architecture of an innovative museum information system, as well as its implementation details is presented. In particular the requirements and the system architecture are presented along with the problems that were encountered. The main directions of the system design are (a) to increase interoperability levels and therefore assist proactive curation and (b) to enhance navigation by the usage of handheld devices. The first direction is satisfied by the design of a rich metadata schema based on the CIDOC/CRM standard. The second direction is fulfilled by the implementation of a module, which integrates the museum database with a subsystem appropriate to support user navigation into the museum floors and rooms. The module is expressed as a navigation functionality, which is accessed through handheld devices and peripherals, such as PDAs and RFID tags. The proposed system is functional and operates into the Solomos Museum, situated in Zakynthos island, Greece

Carbon Free Boston: Waste Technical Report

Part of a series of reports that includes: Carbon Free Boston: Summary Report; Carbon Free Boston: Social Equity Report; Carbon Free Boston: Technical Summary; Carbon Free Boston: Buildings Technical Report; Carbon Free Boston: Transportation Technical Report; Carbon Free Boston: Energy Technical Report; Carbon Free Boston: Offsets Technical Report; Available at http://sites.bu.edu/cfb/OVERVIEW: For many people, their most perceptible interaction with their environmental footprint is through the waste that they generate. On a daily basis people have numerous opportunities to decide whether to recycle, compost or throwaway. In many cases, such options may not be present or apparent. Even when such options are available, many lack the knowledge of how to correctly dispose of their waste, leading to contamination of valuable recycling or compost streams. Once collected, people give little thought to how their waste is treated. For Boston’s waste, plastic in the disposal stream acts becomes a fossil fuel used to generate electricity. Organics in the waste stream have the potential to be used to generate valuable renewable energy, while metals and electronics can be recycled to offset virgin materials. However, challenges in global recycling markets are burdening municipalities, which are experiencing higher costs to maintain their recycling. The disposal of solid waste and wastewater both account for a large and visible anthropogenic impact on human health and the environment. In terms of climate change, landfilling of solid waste and wastewater treatment generated emissions of 131.5 Mt CO2e in 2016 or about two percent of total United States GHG emissions that year. The combustion of solid waste contributed an additional 11.0 Mt CO2e, over half of which (5.9 Mt CO2e) is attributable to the combustion of plastic [1]. In Massachusetts, the GHG emissions from landfills (0.4 Mt CO2e), waste combustion (1.2 Mt CO2e), and wastewater (0.5 Mt CO2e) accounted for about 2.7 percent of the state’s gross GHG emissions in 2014 [2]. The City of Boston has begun exploring pathways to Zero Waste, a goal that seeks to systematically redesign our waste management system that can simultaneously lead to a drastic reduction in emissions from waste. The easiest way to achieve zero waste is to not generate it in the first place. This can start at the source with the decision whether or not to consume a product. This is the intent behind banning disposable items such as plastic bags that have more sustainable substitutes. When consumption occurs, products must be designed in such a way that their lifecycle impacts and waste footprint are considered. This includes making durable products, limiting the use of packaging or using organic packaging materials, taking back goods at the end of their life, and designing products to ensure compatibility with recycling systems. When reducing waste is unavoidable, efforts to increase recycling and organics diversion becomes essential for achieving zero waste. [TRUNCATED]Published versio

Regional Data Archiving and Management for Northeast Illinois

This project studies the feasibility and implementation options for establishing a regional data archiving system to help monitor and manage traffic operations and planning for the northeastern Illinois region. It aims to provide a clear guidance to the regional transportation agencies, from both technical and business perspectives, about building such a comprehensive transportation information system. Several implementation alternatives are identified and analyzed. This research is carried out in three phases. In the first phase, existing documents related to ITS deployments in the broader Chicago area are summarized, and a thorough review is conducted of similar systems across the country. Various stakeholders are interviewed to collect information on all data elements that they store, including the format, system, and granularity. Their perception of a data archive system, such as potential benefits and costs, is also surveyed. In the second phase, a conceptual design of the database is developed. This conceptual design includes system architecture, functional modules, user interfaces, and examples of usage. In the last phase, the possible business models for the archive system to sustain itself are reviewed. We estimate initial capital and recurring operational/maintenance costs for the system based on realistic information on the hardware, software, labor, and resource requirements. We also identify possible revenue opportunities. A few implementation options for the archive system are summarized in this report; namely: 1. System hosted by a partnering agency 2. System contracted to a university 3. System contracted to a national laboratory 4. System outsourced to a service provider The costs, advantages and disadvantages for each of these recommended options are also provided.ICT-R27-22published or submitted for publicationis peer reviewe

Costing the ex situ conservation of genetic resources: maize and wheat at CIMMYT

Worldwide, the number of genebanks and the amount of seed stored in them has increased substantially over the past few decades. Most attention is focused on the likely benefits from conservation, but conserving germplasm involves costs whose nature and magnitude are largely unknown. In this paper we compile and use a set of cost data for wheat and maize stored in the CIMMYT genebank to address a number of questions. What is the cost of storing an accession of either crop for one more year, or, equivalently what is the benefit in terms of cost savings from eliminating duplicate accessions from the genebank? Relatedly, what is the cost from introducing a new accession into the genebank, given the decision to store it is revisited after one year? Does it make economic sense for CIMMYT to discard accessions that may be available elsewhere? As an extension of this line of inquiry it is possible to value the benefits from either consolidating genebanks or at least networking existing banks to reduce or eliminate duplicate holdings not needed for backup safety purposes. We present estimates of the size and scale economies evident in the CIMMYT operation as a basis for assessing the economics of consolidation. Genebanks represent a commitment to conserve seeds for the very long-run. In this study we report on these long-run costs for the CIMMYT genebank costs that are sensitive to the interest rate used and the protocols for periodically replenishing accessions that are shared with others or regenerating accessions whose viability gradually diminishes with age.Germplasm conservation., Gene banks, Plant., Maize Breeding., Wheat Breeding., Rate of return.,

Organizing Knowledge in Implementation of Knowledge Management as Strategy for Competitive Bussiness at PT Telkom

This study is entitled Organizing Knowledge in Implementation of Knowledge Management. The research was conducted in bussines organization. The research objectives are to find out new concept in coverage of knowledge by knowledge management implementation at Telkom organizing explicit knowledge ; to analysis personal characteristic knowledge manager. This research use by qualitative methode with case study approach at Telkom Japati 1st street Bandung. Technique of gathering data uses observation, archived record, interview, documentation dan physical ware. From the results of studies that have been done, so the conclusion can be drawn as follows: Knowledge management which is done by making taxonomy based processes and business operations is called as knowledge centers that are stored on the intranet while competency-based stream called virtual competency center. Organizing knowledge in virtual storage by creating taxonomy of knowledge toward process and operating bussines, tree types of knowledge are:Structure knowledge: unstructure knowledge and less structure knowledge. For other media are managed by a special unit that is the library. The technology media support information and communications intended to improve information transfer and sharing of knowledge organization as a whole through cooperation and communication between individuals. Recomendation: It is better to make guidelines of writing articles on KM Tool, in order to avoid a flood of information that is not need. For example the text have been made by others. .It is better also to make the theme of writing, so that the contributors will more focus in creating the knowledge. Therefore, it will give deep exploration a theme. Form of virtual communication in KM should also explore the tacit knowledge. It is appropriate if the contributors are also allowed to create works that are audio-visual format. For example how to use technology in the 3.5 G DAT file format, or how to assemble the satellite Telkom2. Keyword: Business communication; Knowledge management; Organizational Communication; Organizing knowledge; Knowledge strorag