Search results for "PACKAGE"
showing 10 items of 116 documents
Detection of condition-specific marker genes from RNA-seq data with MGFR
2019
The identification of condition-specific genes is key to advancing our understanding of cell fate decisions and disease development. Differential gene expression analysis (DGEA) has been the standard tool for this task. However, the amount of samples that modern transcriptomic technologies allow us to study, makes DGEA a daunting task. On the other hand, experiments with low numbers of replicates lack the statistical power to detect differentially expressed genes. We have previously developed MGFM, a tool for marker gene detection from microarrays, that is particularly useful in the latter case. Here, we have adapted the algorithm behind MGFM to detect markers in RNA-seq data. MGFR groups s…
An Information Systems Design Product Theory for Software Project Estimation and Measurement Systems
2009
There is relatively little research on software Project Estimation and Measurement Systems (PEMS). Commercial PEMS vary in functionality and effective- ness. Their intended users thus do not know what to ex- pect from PEMS and how to evaluate them. This paper creates an information system design product theory for the class of PEMS that prescribes the meta-requirements, the meta-design, and applicable theories for all products within the class. Meta-requirements and the meta-design are derived from the project estimation and measurement literature, experiences obtained during more than ten years of empirical work in Finnish Software Measurement Association, and a commercially available PEMS.
Grounds and Challenges for Implementing a Circular Economy in the European Road transport Sector
2017
Environmental challenges, especially in the form of resource depletion, pollution and greenhouse gas emission, are very important challenges for the socio-economic development. For this reason, the concept of a circular economy has been developed and is being implemented in different areas. In 2015, the European Union adopted the Circular Economy Package consisting of an “EU Action Plan for the Circular Economy”, presenting a set of actions aimed at achieving objectives of the circular economy in Europe. The goal of the paper is to describe and discuss key challenges facing implementation of the concept of the circular economy in the European road transport sector. First, the concept of a c…
FMI4j: A Software Package for working with Functional Mock-up Units on the Java Virtual Machine
2018
This paper introduces FMI4j, a software package for working with Functional Mock-up Units (FMUs) on the Java Virtual Machine (JVM). FMI4j is written in Kotlin, which is 100% interoperable with Java, and consists of programming APIs for parsing the meta-data associated with an FMU, as well as running them. FMI4j is compatible with FMI version 2.0 for Model Exchange (ME) and Co-Simulation (CS). Currently, FMI4j is the only software library targeting the JVM supporting ME 2.0. In addition to provide bare-bones access to such FMUs, it provides the means for solving them using a range of bundled fixedand variable-step solvers. A command line tool named FMU2Jar is also provided, which is capable …
A Software Package for a Serum Bank Management
1979
A serum-bank is a collection of human serum samples coming from different locations (in our case Children Hospital, schools, factories, town departemens), allocated in some archives. Principal users of a such data-bank are, of course, physicians and biologists that are mainly interested in statistical analysis (computation of averages, variances factor analysis, etc.) of immunological and epidemiological relevance, in order to investigate about some haematochemical parameters common to some selected subset of the archives [1], [2].
The Detector Control of the PANDA Experiment
2014
The PANDA experiment will be built at the antiproton storage ring HESR, a part of the new accelerator facility FAIR in Darmstadt, Germany. PANDA aims amongst other topics for high precision measurements in hadron spectroscopy and search for exotic matter. To guarantee the high resolution of the different components a detector control system (DCS) monitoring temperatures, humidity, pressure, and controlling chillers and power supplies is needed. The DCS of PANDA is built using the open-source software package EPICS (Experimental Physics and Industrial Control System) with a PANDA specific version of Control-System Studio. In this document the general concepts of the PANDA DCS will be discuss…
Density-functional tight-binding for beginners
2009
This article is a pedagogical introduction to density-functional tight-binding (DFTB) method. We derive it from the density-functional theory, give the details behind the tight-binding formalism, and give practical recipes for parametrization: how to calculate pseudo-atomic orbitals and matrix elements, and especially how to systematically fit the short-range repulsions. Our scope is neither to provide a historical review nor to make performance comparisons, but to give beginner's guide for this approximate, but in many ways invaluable, electronic structure simulation method--now freely available as an open-source software package, hotbit.
An updated version of the computational package SIMPRE that uses the standard conventions for Stevens crystal field parameters
2014
The crystal field approach used by SIMPRE is analyzed, verifying the exactness of the results concerning energy levels and magnetic properties calculated by the package. To coincide with the prevailing conventions, we reformulate the presentation of the crystal field parameters, so that the results are now, also from a formal point of view, strictly correct. New calculations are presented to test the influence of neglecting the excited J states, a common but critical approximation employed by SIMPRE. For that, we examine the case of Er(trensal) complex (H3 trensal = 2,2',2″-tris(salicylideneimino)triethylamine) where the influence of this approximation is found to be minimal. A patched vers…
Comprehensive System for Systematic Case-Driven Software Reuse
2010
Reuse of software artifacts (blueprints and code) is normally associated with organising a systematic reuse framework most often constructed for a specific problem domain. In this paper we present a system (language, tool, reuse process) where software reuse is based on building and retrieving of so-called software cases (large compound artifacts) that can be reused between domains. The system is opportunistic in that software cases result from usual (non-reuse oriented) activities where also semantic information is added. This information is used to support regular development but may serve later to retrieve software cases. Having this common semantic basis, we can organise a systematic cr…
Energy performance improvements of a DEC system due to wet heat exchangers
2011
This work concerns an innovative desiccant and evaporative cooling (DEC) system for building air conditioning. The original system is an experimental DEC air handling unit installed at the Solar Laboratory of the University of Palermo and recently modified and updated. With the aim to increase the cooling effect due to water evaporation in the return air flow rate, the sensible heat exchanger was replaced with two cross flow flat plate heat exchangers installed in series, with continuous humidification of the secondary air flow. The new thermodynamic cycle is theoretically described and the realization of the real application is shown. Detailed operational data and energy performance indica…