CFinder: locating cliques and overlapping modules in biological networks

Most cellular tasks are performed not by individual proteins, but by groups of functionally associated proteins, often referred to as modules. In a protein association network modules appear as groups of densely interconnected nodes, also called communities or clusters. These modules often overlap with each other and form a network of their own, in which nodes (links) represent the modules (overlaps). We introduce CFinder, a fast program locating and visualizing overlapping, densely interconnected groups of nodes in undirected graphs, and allowing the user to easily navigate between the original graph and the web of these groups. We show that in gene (protein) association networks CFinder can be used to predict the function(s) of a single protein and to discover novel modules. CFinder is also very efficient for locating the cliques of large sparse graphs. Availability: CFinder (for Windows, Linux and Macintosh) and its manual can be downloaded from http://angel.elte.hu/clustering. Supplementary information: Supplementary data are available on Bioinformatics online.     

SAGEmap分析及DNA序列染色体定位的电子自动化实现

通过一组Perl模块(命名为SLtools)实现自动化SAGEmap序列表达谱分析及核酸序列的自动化染色体定位分析,从而使这两种重要的生物学功能的高通量分析成为可能。程序具有良好的可移植性和适应性,可以直接在Windows和Linux系统下使用,无须作任何改动。只须简单编写Perl程序,向该模块提交核酸序列或者序列注册号,就可以得到一系列相应的分析结果。模块可以免费下载:http://bioinfor.cicams.ac.cn/SLtools.tar.gz。     

AmberFFC, a flexible program to convert AMBER and GLYCAM force fields for use with commercial molecular modeling packages

A program for converting the different existing AMBER and GLYCAM force fields for use with commercial molecular modeling packages is presented, using the Molecular Simulations Inc. (MSI or Accelrys) software package as a case model. Called AmberFFC, the program creates AMBER and GLYCAM force field files suitable for use with the Accelrys molecular mechanics modules by transforming the amino acid, nucleotide, and monosaccharide topology databases and force field parameter files to the Accelrys file format. It is intended for any modeler who is interested in using the current AMBER and GLYCAM force fields with the Accelrys FDiscover and CDiscover programs. AmberFFC has been written entirely with the Perl programming language, making it highly flexible and portable. In order to compare the implementation of the force fields converted by AmberFFC in the Accelrys package with their corresponding execution in the AMBER software, and also to verify the efficiency of the AmberFFC program, results from single point energy calculations for 13 model molecules were obtained with the two programs. It is demonstrated that results obtained with the CDiscover and FDiscover modules compare well to those found using Sander_classic, thus showing that AmberFFC is a highly efficient program. Some energy differences between the AMBER and Accelrys software have been observed, and their origin has been characterized and discussed.     

Representation of a protein molecule as a tree and application to modular computer programs which calculate and modify atomic coordinates

The concept and representation of a logical tree as defined in computer science is applied to obtain a suitable representation of protein molecules in computer programs which handle or calculate atomic coordinates of protein molecules. On the basis of this analysis and of the analysis of the calculation and modification of the structure of a protein from bond lengths, bond angles, and dihedral angles, which is reproduced in an appendix, program modules which accomplish the various required computations are described. Three such modules are given in Iverson notation; in fact, it is hoped that this article will serve as a reasonably complete basis for the preparation of machine programs by moderately proficient programmers.     

The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks

The SBML ODE Solver Library (SOSlib) is a programming library for symbolic and numerical analysis of chemical reaction network models encoded in the Systems Biology Markup Language (SBML). It is written in ISO C and distributed under the open source LGPL license. The package employs libSBML structures for formula representation and associated functions to construct a system of ordinary differential equations, their Jacobian matrix and other derivatives. SUNDIALS' CVODES is incorporated for numerical integration and sensitivity analysis. Preliminary benchmarking results give a rough overview on the behavior of different tools and are discussed in the Supplementary Material. The native application program interface provides fine-grained interfaces to all internal data structures, symbolic operations and numerical routines, enabling the construction of very efficient analytic applications and hybrid or multi-scale solvers with interfaces to SBML and non SBML data sources. Optional modules based on XMGrace and Graphviz allow quick inspection of structure and dynamics.     

昆虫飞行模拟监控系统设计

本文根据昆虫飞行的特点,模拟昆虫飞行的实验装置,由飞行磨、单片机及微型计算机组成,编辑设计飞行监控软件,该程序分为三个模块：系统监控程序模块;时钟程序模块和信号处理程序模块。利用微机适时采集飞行数据,记录和分析监测结果,模拟昆虫的飞行速度和持续时间。     

SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling

Label-free quantification of high mass resolution LC-MS data has emerged as a promising technology for proteome analysis. Computational methods are required for the accurate extraction of peptide signals from LC-MS data and the tracking of these features across the measurements of different samples. We present here an open source software tool, SuperHirn, that comprises a set of modules to process LC-MS data acquired on a high resolution mass spectrometer. The program includes newly developed functionalities to analyze LC-MS data such as feature extraction and quantification, LC-MS similarity analysis, LC-MS alignment of multiple datasets, and intensity normalization. These program routines extract profiles of measured features and comprise tools for clustering and classification analysis of the profiles. SuperHirn was applied in an MS1-based profiling approach to a benchmark LC-MS dataset of complex protein mixtures with defined concentration changes. We show that the program automatically detects profiling trends in an unsupervised manner and is able to associate proteins to their correct theoretical dilution profile.     

Wallacea and its nectarivorous birds: nestedness and modules

Aim Wallacea, the vast oceanic boundary between the Oriental and Australian regions, contains 122 true nectarivorous bird species. It is the contact zone of the Oriental sunbirds and the Australian honeyeaters, and at least three more true nectarivorous families are resident in the region. An island–bird matrix for Wallacea was tested for the presence of two patterns, nestedness and modularity. If the matrix is modular, it consists of a number of densely linked subgroups or modules of islands and birds, which are weakly interconnected. These modules are used as a new tool in analysing biogeographical boundaries in Wallacea. Location Wallacea, Indonesia. Methods We constructed an island–bird matrix for Wallacea and used two algorithms, aninhado and sa , to test it for nestedness and modularity, respectively. aninhado calculates the matrix temperature and provides a null model, and sa is a module‐detecting program based on simulated annealing. The results of the sa were compared with those from a hierarchical cluster analysis. Results The matrix had a nested pattern, as is commonly the case for island–species matrices. The SA detected four modules in Wallacea, each consisting of a group of islands sharing a group of nectarivorous birds. The sa algorithm produced a more detailed pattern of the area than did the hierarchical cluster analysis. Main conclusions Modularity and nestedness do not preclude each other as biogeographical patterns. The boundaries of the modules detected by sa compared well with major boundaries from the existing literature and showed a clear division of Wallacea into modules of birds and islands closely linked together. Thus modules are biogeographical units of islands sharing a specific nectarivorous fauna. For some research questions, we suggest that modules may be more appropriate biogeographical units than single islands or traditionally perceived archipelagos. The nectarivorous families showed distinctly different distributions, indicating variation in their colonization history and speciation processes. We recommend sa as a tool for detecting fine‐grained biogeographical patterns.     

PNME – A gene-gene parallel network module extraction method

In the domain of gene-gene network analysis, construction of co-expression networks and extraction of network modules have opened up enormous possibilities for exploring the role of genes in biological processes. Through such analysis, one can extract interesting behaviour of genes and would help in the discovery of genes participating in a common biological process. However, such network analysis methods in sequential processing mode often have been found time-consuming even for a moderately sized dataset.It is observed that most existing network construction techniques are capable of handling only positive correlations in gene-expression data whereas biologically-significant genes exhibit both positive and negative correlations. To address these problems, we propose a faster method for construction and analysis of gene-gene network and extraction of modules using a similarity measure which can identify both negatively and positively correlated co-expressed patterns. Our method utilizes General-purpose computing on graphics processing units (GPGPU) to provide fast, efficient and parallel extraction of biologically relevant network modules to support biomarker identification for breast cancer. The modules extracted are validated using p-value and q-value for both metastasis and non-metastasis stages of breast cancer. PNME has been found capable of identifying interesting biomarkers for this critical disease. We identified six genes with the interesting behaviours which have been found to cause breast cancer in homo-sapiens.     

Exercise, nutrition and you: an off-campus course for grades 2-12

Since interest in science classes has declined recently and obesity, especially in youth, continues to increase, an exercise physiology-based course was taught in public parks to promote active-learning science and healthy living. The course emphasized and integrated exercise, nutrition, and health during a 3-h session. Following an introduction, five hands-on laboratory-based student modules were performed. Students performed respiratory, cardiovascular, temperature regulation, energy expenditure, oxygen uptake, and exercise modules. During most modules, the students made measurements at rest and during the performance of exercise at different intensities. The students were very involved and engaged in problem solving throughout the session. The program was given for 10 days to more than 500 students representing 18 classes from 10 different schools. Evaluations indicated that the program was a real-life science experience that gave the students a new understanding of how their bodies worked and the purpose of exercise. The students and teachers also experienced "school learning" put into action as the program fit well with their science curriculum.     

TREECON: A software package for the construction and drawing of evolutionary trees

A package of programs (run by a management program called TREECON)was developed for the construction and drawing of evolutionarytrees. The program MATRIX calculates dissimilarity values andcan perform bootstrap analysis on nucleic acid sequences. TREEimplements different evolutionary tree constructing methodsbased on distance matrices. Because some of these methods produceunrooted evolutionary trees, a program ROOT places a root onthe tree. Finally, the program DRAW draws the evolutionary tree,changes its size or topology, and produces drawings suitablefor publication. Whereas MATRIX is suited only for nucleic acids,the modules TREE, ROOT and DRAW are applicable to any kind ofdissimilarity matrix. The programs run on IBM-compatible microcomputersusing the DOS operating system.     

Basic Training Program in Medical Pedagogy: a 1-year program for medical faculty.

In 1979 université de Montréal developed the Basic Training Program in Medical Pedagogy; the program has since been offered at two other Canadian medical schools. The learning activities are spread over an academic year so that the teachers are able to continue their clinical or research duties. The program, which follows a model of systematic instruction, comprises 17 self-instructional modules on basic educational topics adapted to medical teaching. The topics are related to four components of an integrated system: student needs and learning objectives, instructional methods, student evaluation and program evaluation. The instructional format is aimed at three levels--understanding, analysis and application--to which assignments and assessments are related. In addition to the modules, the program offers 15 half-day sessions for small groups (five participants and one instructor) to discuss aspects of the program, especially home assignments and the application of personal educational projects. A minimum of 100 hours of personal time is requested. The program''s main goal is that students be placed at the centre of the educational process. Of 215 participants since 1979, 171 (80%) have completed the program and reported high satisfaction. Issues related to any faculty development program are discussed.     

SEARCHPKS: A program for detection and analysis of polyketide synthase domains

SEARCHPKS is a software for detection and analysis of polyketide synthase (PKS) domains in a polypeptide sequence. Modular polyketide synthases are unusually large multi-enzymatic multi-domain megasynthases, which are involved in the biosynthesis of pharmaceutically important natural products using an assembly-line mechanism. This program facilitates easy identification of various PKS domains and modules from a given polypeptide sequence. In addition, it also predicts the specificity of the potential acyltransferase domains for various starter and extender precursor units. SEARCHPKS is a user-friendly tool for correlating polyketide chemical structures with the organization of domains and modules in the corresponding modular polyketide synthases. This program also allows the user to extensively analyze and assess the sequence homology of various polyketide synthase domains, thus providing guidelines for carrying out domain and module swapping experiments. SEARCHPKS can also aid in identification of polyketide products made by PKS clusters found in newly sequenced genomes. The computational approach used in SEARCHPKS is based on a comprehensive analysis of various characterized clusters of modular polyketide synthases compiled in PKSDB, a database of modular polyketide synthases. SEARCHPKS can be accessed at http://www.nii.res.in/searchpks.html.     

Software for machine-independent quantitative interpretation of SSCP in capillary array electrophoresis (QUISCA)

PCR single-stranded conformational polymorphism (SSCP) analysis is a simple and rapid electrophoretic technique for the sensitive detection of sequence variants of PCR products. Here we describe a cross-platform program package, quantitative interpretation of SSCP in capillary array (QUISCA), which allows semi-automated quantitative detection of sequence variants separated by multicolor fluorescence-based SSCP electrophoresis using various capillary array apparatus. The program, together with the QUISCAview as a graphical user interface, takes trace data in ASCII format and processes them with three modules: signal denoising/baseline subtraction, color-matrix construction/application, and calibration of peak positions between multiple capillary runs using internal standard peaks. QUISCA is compatible with data from various widely used capillary array sequencers and is suitable not only for finding or typing SNPs in individual DNAs but also for the accurate estimation of the allele frequencies of many SNPs using a pooled DNA strategy. QUISCA can also serve as a versatile core program for various fragment analyses.     

Katalyst: development of a fifth-grade novel approach to health and science experiential learning

The Katalyst intervention program was piloted in fifth-grade classrooms at two Appalachian schools during the 2017–18 academic year as a potential educational resource to tackle the rising rates of obesity and chronic diseases in this region. The program consisted of four 60-minute modules, each based on a specific organ system. Each module incorporated hands-on lessons in physiology with an emphasis on preventing chronic disease through diet, nutrition, physical activity, and abstinence from drug and tobacco use. The modules were led by medical students and undergraduate volunteers who completed a two-day training. A 37-item survey assessing knowledge and perceptions regarding healthy lifestyles was administered to fifth grade participants prior to and following the intervention in order to assess the impact of the program. Additionally, educators at intervention schools were given a questionnaire post-intervention to provide feedback on the program. This paper describes the rationale, program design and execution, and conclusion of the Katalyst intervention program. It is anticipated that this program will reinforce current educational standards regarding diet, nutrition and physical activity in order to empower target students to establish healthy lifestyle behaviors and that programs modeled after the Katalyst curriculum may serve as a novel, viable option to health educators.