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This paper describes Stata command lclogit2, an enhanced version of lclogit (Pacifico and Yoo, 2013). Like its predecessor, lclogit2 uses the Expectation-Maximization (EM) algorithm to estimate latent class conditional logit (LCL) models. But it executes the EM algorithm's core algebraic operations in Mata, and runs considerably faster as a result. It also allows linear constraints on parameters to be imposed in a more convenient and flexible manner. It comes with parallel command lclogitml2, a new standalone program that uses gradient-based algorithms to estimate LCL models. Both lclogit2 and lclogitml2 are supported by a new postestimation tool, lclogitwtp2, that evaluates willingness-to-pay measures implied by estimated LCL models.

Software implementations of thermodynamic property routines for ammonia-water mixtures are developed for refrigeration and air-conditioning applications. Saturation correlations are employed to identify single-phase state points, yielding up to a 5-fold reduction in property evaluation time. A run-time database of previously evaluated state points is implemented to improve initial guesses for iterative property evaluation, reducing property evaluation time by 45% in a representative study. The property routines are implemented in a standalone program and as a compiled routine for use in MATLAB® and Simulink®. Both implementations perform property evaluations significantly faster than existing software packages. Program performance is measured on a 2.2 GHz machine, and average individual state point evaluation times were found to range from 50 to 930 µs, depending on the provided input properties. Additionally, a segmented, transient, ammonia-water absorber model is developed in Simulink® to assess the use of the property routines for practical engineering calculations. The proposed computational techniques can be applied to accelerate property evaluations for other mixtures.

Eucb is a standalone program for geometrical analysis of molecular dynamics trajectories of protein systems. The program is written in GNU C++ and it can be installed in any operating system running a C++ compiler. The program performs its analytical tasks based on user supplied keywords. The source code is freely available from http://stavrakoudis.econ.uoi.gr/eucb under LGPL 3 license. Program summary Program title: Eucb Catalogue identifier: AEIC_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEIC_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 31 169 No. of bytes in distributed program, including test data, etc.: 297 364 Distribution format: tar.gz Programming language: GNU C++ Computer: The tool is designed and tested on GNU/Linux systems Operating system: Unix/Linux systems RAM: 2 MB Supplementary material: Sample data files are available Classification: 3 Nature of problem: Analysis of molecular dynamics trajectories. Solution method: The program finds all possible interactions according to input files and the user instructions. Then it reads all the trajectory frames and finds those frames in which these interactions occur, under certain geometrical criteria. This is a blind search, without a priori knowledge if a certain interaction occurs or not. The program exports time series of these quantities (distance, angles, etc.) and appropriate descriptive statistics. Running time: Depends on the input data and the required options.

Electron microscopy has been used to measure the mass of biological nanoparticles since the early 60s, and is the only way to obtain the mass of large structures or parameters such as the mass-per-length of filaments. The ability of this method to sort heterogeneous samples both in terms of mass and shape promises to make it a key tool for proteomics down to the single cell level. A new multiplatform software package, MASDET, that can be run under MATLAB or as a standalone program is described. Based on a user-friendly graphical interface MASDET streamlines mass evaluation and greatly increases the speed of required optimisation procedures. Importantly, the immediate application of Monte-Carlo simulations to describe multiple scattering is possible, allowing the mass analysis of thicker samples and the generation of mass thickness maps.

RNA interference (RNAi) is a popular and effective method for silencing gene expression. siRNAs should be gene-specific and effective to achieve specific and potent gene silencing. However, most currently available siRNA design programs are web-based programs that either require each sequence be submitted individually, making large-batch analyses difficult to conduct, or only provide limited options for searching off-target candidates (e.g. NCBI-BLAST). We have developed a stand-alone, enhanced RNAi design program that overcomes these shortcomings. We have implemented WU-BLAST, FASTA and SSEARCH homology searches for siRNA candidates to improve gene specific siRNA selection and to identity siRNA candidates that could lead to off-target gene silencing. We also included many new features such as siRNA score calculation and calculation of siRNA internal stability to help select highly potent siRNAs. This program is freely available for academic and commercial use (ftp://ftp.systemsbiology.net/pub/blin/SiRNA/), and can be installed and run on any Linux machine. Our program automates the search for siRNAs and the resulting data files including a list of siRNA primers with scores and database search results for each siRNA candidate are stored locally for easy retrieval and inspection when needed.

The paper describes the design and implementation of a distributed Ada system. Ada is not well defined with respect to distribution, and any implementation for distributed execution must make a number of decisions about the language. The objectives in the implementation described here are to remain as close to the current definition of Ada as possible, and to learn through experience what changes are necessary in future versions of the language. The approach taken to distributing a single program is to assign library units that compose it to nodes of the distributed system. In a formal sense the semantics of a program is independent of the distribution because the semantics is interpreted to include all possible behaviours that result from different distributions. However, the functionality of the distributed program may then depend on the distribution in the sense that program behaviour may be impacted by the time required for communication among the distributed modules, or parts of the program may continue to function in presence of failures. The implementation technique converts each distributed module into a standalone program that communicates with its correspondents; each of these may then be compiled by an existing Ada compiler. Issues discussed include the ramifications of sharing of data types, objects, subprograms, tasks, and task types. The implementation techniques used in the translator are described.

A procedure is described for the generation of a variety of molecular surfaces using a ‘bit’ lattice, and avoiding the computational load imposed by geometric techniques. The procedure is well suited to minicomputers used to host calligraphic displays, and is flexible in terms of resolution and size of surface, and permits several styles of display. The procedure may be used as a standalone program, or as part of a real-time molecular manipulation system.