Bifurcation discovery tool

MOTIVATION: Biochemical networks often yield interesting behavior such as switching, oscillation and chaotic dynamics. This article describes a tool that is capable of searching for bifurcation points in arbitrary ODE-based reaction networks by directing the user to regions in the parameter space, where such interesting dynamical behavior can be observed. RESULTS: We have implemented a genetic algorithm that searches for Hopf bifurcations, turning points and bistable switches. The software is implemented as a Systems Biology Workbench (SBW) enabled module and accepts the standard SBML model format. The interface permits a user to choose the parameters to be searched, admissible parameter ranges, and the nature of the bifurcation to be sought. The tool will return the parameter values for the model for which the particular behavior is observed. AVAILABILITY: The software, tutorial manual and test models are available for download at the following website: http:/www.sys-bio.org/ under the bifurcation link. The software is an open source and licensed under BSD.     

The pebble tool or chopper/chopping tool industry in China

Several paleolithic sites (or localities) with cultural characteristics in common have been found in South China in recent years. They are paleolithic sites in Beise, Guangxi; in the upper reaches of the Han River, Shaanxi; Shuiyang River, Anhui; Li River and Yuan River, Human; Liao River, Jiangxi; etc.. The sites show some similarities in the stone tool industry which are as follows; large tools are more common than small ones; pebble tools are more common than flakes; and the chopper/chopping tools are more common than scrapers. This indicates that the paleolithic cultures in South China are part of the pebble tool — chopper/chopping tool tradition which is similar to that in Southeast Asia, but has many differences in certain aspects from the culture of North China. The area where the sites have been found covers large parts of Southeast China, including the Yangtze River valley (23°50′–33°5′ N, 104°38′–119° E).     

SENSE tool: easy-to-use web-based tool to calculate food product environmental impact

Purpose

The purpose of the European SENSE project was to define an integral system to assess and communicate the environmental impacts of food products and to develop a web-based tool for Small and Medium size Enterprises (SMEs). The tool has been tested in salmon, beef-and-dairy, and fruit juice production sectors.

Methods

The SENSE project has evaluated several existing methodologies for environmental impact assessment over the life cycle including also social aspects, in order to deliver a new integral system for the environmental and social assessment of agricultural and aquaculture food products.

Results and discussion

The system includes a standardization of a data gathering system, a selection of relevant key environmental performance indicators for food supply chains and a common methodology to perform simplified life cycle impact assessment. The results are based on collected information on the use of resources and emissions generated along the supply chain of food or drink products. The main result is a web-based software tool that is based on a summation of the partial impacts of the different steps in food supply chains. In this software, different actors in the supply chain can enter their own data and link them to the data of other companies. The results obtained in the tool could be used for at least six different approaches: (i) environmental impact assessment of the product, (ii) food chain hot spot identification, (iii) comparison of hypothetical or real improvement scenarios, (iv) assessment of the environmental impact development over the years, (v) benchmarking opportunity for the companies, and (vi) a business to business communication strategy. The scientific robustness of the tool has been tested comparing the obtained results with the same analysis with commercial software.

Conclusions

The SENSE tool is a simplified tool designed for food and drink SMEs to assess their sustainability on their own. This cannot be fully compared to a complete LCA study. The testing with SMEs showed that they need additional support for filling in the questionnaires correctly and interpret the results. The simplified evaluation of environmental impacts based on a life cycle approach could lead to benefits to SMEs within the food industry. The future application and development of the tool will be focused on adapting the tool to the Product Environmental Footprint initiative requirements and self-assessment opportunities.

     

MACAT--microarray chromosome analysis tool

SUMMARY: By linking differential gene expression to the chromosomal localization of genes, one can investigate microarray data for characteristic patterns of expression phenomena involving sizeable parts of specific chromosomes. We have implemented a statistical approach for identifying significantly differentially expressed chromosome regions. We demonstrate the applicability of the approach on a publicly available data set on acute lymphocytic leukemia. AVAILABILITY: The R-package MACAT can be obtained from http://www.compdiag.molgen.mpg.de/software/macat.shtml SUPPLEMENTARY INFORMATION: http://www.compdiag.molgen.mpg.de/software/macat.shtml.     

Mlab--a mathematical modeling tool

An interactive interpreter called Mlab is described. One uses Mlab by typing commands. In this sense, Mlab is a programming language. It has various mathematical and graphical facilities which make it a useful tool for mathematical modeling. The curve fitting capabilities of Mlab are augmented with differential-equation-handling and matrix-manipulation capabilities which provide a powerful and civilized facility for curve fitting. Many people are engaged in this activity, and, in general, they use programs which are neither sufficiently general nor easy to use. (Some conventional programming is usually required, for example.) Mlab purports to be easier than alternate approaches. The nature of Mlab is discussed with accompanying examples. The main example is the use of curve fitting to determine molecular weight from ultracentrifuge data. This example was chosen because it exhibits a special feature of Mlab, namely the root operator, which appears in the definition of the model function.     

DNA-guided genome editing tool

正Technologies for targeted modification of eukaryotic genomes are of great value for elucidating and manipulating gene functions in fundamental and applied biological research.In the past two decades,genome editing tools have evolved quickly from random DNA mutagenesis-inducing chemicals or ionizing radiation to programmable sequencespecific nucleases(SSNs)with the CRISPR/Cas technology as the most significant breakthrough(Gaj et al.,2013).     

ACGT-a comparative genomics tool

SUMMARY: ACGT (a comparative genomics tool) is a genomic DNA sequence comparison viewer and analyzer. It can read a pair of DNA sequences in GenBank, Embl or Fasta formats, with or without a comparison file, and provide users with many options to view and analyze the similarities between the input sequences. It is written in Java and can be run on Unix, Linux and Windows platforms. AVAILABILITY: The ACGT program is freely available with documentation and examples at website: http://db.systemsbiology.net/projects/local/mhc/acgt/     

MD simulation of tool wear behaviour based on changes of tool rake and flank angle caused by diamond tool position adjustment

A new method for adjusting the tool rake and flank angles by changing the position of the tools was used to explore the behaviour of wear using MD simulation. In this paper, a new improved tool was used and found to have lower wear compared to conventional tools. Simulations under the same cutting conditions were carried out using a tool swinging to six different rake angles of six different adjustment angles. Further analysis of the influence of different adjustment angles on the wear behaviour of the tool by cutting force, friction coefficient, temperature, radial distribution function and wear rate was conducted. The highest normal force was observed with the tool swung to ?15°, and the tangential force did not produce any significant changes. The friction coefficients were also not observed as a linear change with the increasing angle of adjustment. At the same time, the particularities and differences at ?15° were illustrated, from the most intuitive tool flank wear images. Finally, the causes of this phenomenon were further explained in terms of temperature and radial distribution function and the correctness of this phenomenon was proved, which is different from previous researches.     

Modelling as a tool

Conclusion The three examples mentioned, illustrate some kinds of mathematical modelling. These were all models of isolated sub-systems. The impression may exist that it is not yet possible to model the total algal assemblage. This possibility however, depends on the aim of the model. When the aim is to predict the maximum biomass, the model of LOS (1980) can be used. When prediction of the actual biomass as well as the transition states from one maximum to the other is aimed, there is still work to be done. The same applies when one wants a model that predicts zooplankton and fish too.In general the aim determines the kind of model. A multidisciplinary team of physicians, chemists, biologists and mathematicians have to build it.     

DAVID gene ID conversion tool

Our current biological knowledge is spread over many independent bioinformatics databases where many different types of gene and protein identifiers are used. The heterogeneous and redundant nature of these identifiers limits data analysis across different bioinformatics resources. It is an even more serious bottleneck of data analysis for larger datasets, such as gene lists derived from microarray and proteomic experiments. The DAVID Gene ID Conversion Tool (DICT), a web-based application, is able to convert user's input gene or gene product identifiers from one type to another in a more comprehensive and high-throughput manner with a uniquely enhanced ID-ID mapping database.     

AuberGene--a sensitive genome alignment tool

MOTIVATION: The accumulation of genome sequences will only accelerate in the coming years. We aim to use this abundance of data to improve the quality of genomic alignments and devise a method which is capable of detecting regions evolving under weak or no evolutionary constraints. RESULTS: We describe a genome alignment program AuberGene, which explores the idea of transitivity of local alignments. Assessment of the program was done based on a 2 Mbp genomic region containing the CFTR gene of 13 species. In this region, we can identify 53% of human sequence sharing common ancestry with mouse, as compared with 44% found using the usual pairwise alignment. Between human and tetraodon 93 orthologous exons are found, as compared with 77 detected by the pairwise human-tetraodon comparison. AuberGene allows the user to (1) identify distant, previously undetected, conserved orthogonal regions such as ORFs or regulatory regions; (2) identify neutrally evolving regions in related species which are often overlooked by other alignment programs; (3) recognize false orthologous genomic regions. The increased sensitivity of the method is not obtained at the cost of reduced specificity. Our results suggest that, over the CFTR region, human shares 10% more sequence with mouse than previously thought ( approximately 50%, instead of 40% found with the pairwise alignment).