TOPPAS: a graphical workflow editor for the analysis of high-throughput proteomics data

Mass spectrometry coupled to high-performance liquid chromatography (HPLC-MS) is evolving more quickly than ever. A wide range of different instrument types and experimental setups are commonly used. Modern instruments acquire huge amounts of data, thus requiring tools for an efficient and automated data analysis. Most existing software for analyzing HPLC-MS data is monolithic and tailored toward a specific application. A more flexible alternative consists of pipeline-based tool kits allowing the construction of custom analysis workflows from small building blocks, e.g., the Trans Proteomics Pipeline (TPP) or The OpenMS Proteomics Pipeline (TOPP). One drawback, however, is the hurdle of setting up complex workflows using command line tools. We present TOPPAS, The OpenMS Proteomics Pipeline ASsistant, a graphical user interface (GUI) for rapid composition of HPLC-MS analysis workflows. Workflow construction reduces to simple drag-and-drop of analysis tools and adding connections in between. Integration of external tools into these workflows is possible as well. Once workflows have been developed, they can be deployed in other workflow management systems or batch processing systems in a fully automated fashion. The implementation is portable and has been tested under Windows, Mac OS X, and Linux. TOPPAS is open-source software and available free of charge at http://www.OpenMS.de/TOPPAS .     

GradientOptimizer: An open‐source graphical environment for calculating optimized gradients in reversed‐phase liquid chromatography

We here present GradientOptimizer, an intuitive, lightweight graphical user interface to design nonlinear gradients for separation of peptides by reversed‐phase liquid chromatography. The software allows to calculate three types of nonlinear gradients, each of them optimizing a certain retention time distribution of interest. GradientOptimizer is straightforward to use, requires minimum processing of the input files, and is supported under Windows, Linux, and OS X platforms. The software is open‐source and can be downloaded under an Apache 2.0 license at https://github.com/statisticalbiotechnology/NonlinearGradientsUI .     

DAMBE: software package for data analysis in molecular biology and evolution

DAMBE (data analysis in molecular biology and evolution) is an integrated software package for converting, manipulating, statistically and graphically describing, and analyzing molecular sequence data with a user-friendly Windows 95/98/2000/NT interface. DAMBE is free and can be downloaded from http://web.hku.hk/~xxia/software/software.htm. The current version is 4.0.36.     

An affordable approach to interactive desktop molecular modeling

The amazing revolution in computer hardware performance and cost reduction has yet to be carried over to computer software. In fact, application software today is often more expensive and less reliable than the hardware. New enhancements in software development techniques, such as object oriented programming and interactive graphics based user interface design, finally may be having a significant impact on the time-to-market and reliability of these application programs. We discuss our experiences using one such set of software development tools available on the NeXT workstation and describe the effort required to port our MidasPlus molecular modeling package to the NeXT workstation.     

R/Bioconductor在Affymetrix表达芯片中的应用

R是用于统计计算和数据作图的编程语言和程序设计环境,能在多种平台下编译和运行。Bioconductor也是免费开源的程序设计环境,它主要基于统计编程语言R,用于基因组数据的分析。我们通过已发表的数据,包含斑马鱼心肌再生的生物芯片数据,分析源码实例,较为详细地介绍和讲解了R/BioConductor的用法,为推广优秀的免费统计软件提供了一个简单的中文使用手册。     

DrugViz: a Cytoscape plugin for visualizing and analyzing small molecule drugs in biological networks

SUMMARY: DrugViz is a Cytoscape plugin that is designed to visualize and analyze small molecules within the framework of the interactome. DrugViz can import drug-target network information in an extended SIF file format to Cytoscape and display the two-dimensional (2D) structures of small molecule nodes in a unified visualization environment. It also can identify small molecule nodes by means of three different 2D structure searching methods, namely isomorphism, substructure and fingerprint-based similarity searches. After selections, users can furthermore conduct a two-side clustering analysis on drugs and targets, which allows for a detailed analysis of the active compounds in the network, and elucidate relationships between these drugs and targets. DrugViz represents a new tool for the analysis of data from chemogenomics, metabolomics and systems biology. AVAILABILITY: DrugViz and data set used in Application are freely available for download at http://202.127.30.184:8080/software.html.     

Computing graphlet signatures of network nodes and motifs in Cytoscape with GraphletCounter

Biological network analysis can be enhanced by examining the connections between nodes and the rest of the network. For this purpose we have developed GraphletCounter, an open-source software tool for computing graphlet degree signatures that can operate on its own or as a plug-in to the network analysis environment Cytoscape. A unique characteristic of GraphletCounter is its ability to compute the graphlet signatures of network motifs, which can be specified by files generated by the motif-finding tool mfinder. GraphletCounter displays graphlet signatures for visual inspection within Cytoscape, and can output graphlet data for integration with larger workflows. AVAILABILITY AND IMPLEMENTATION: GraphletCounter is implemented in Java. It can be downloaded from the Cytoscape plugin repository, and is also available at http://sonmezsysbio.org/software/ graphletcounter.     

Interactive program for visualization and modelling of proteins,nucleic acids and small molecules

The graphics package Insight for the DEC VAX and Evans and Sutherland PS300, created as part of a joint university-industry research project, provides a broad set of capabilities which allow the user to display molecular models in stick figure and surface representation. The Insight program allows the user to model and manipulate proteins, nucleic acids and small molecules. The software accepts coordinate input from several possible sources and provides both a command and menu interface for manipulation of the graphics objects. The command language and program structure make it easy for the biochemist or molecular biologist to use.     

GenePro: a Cytoscape plug-in for advanced visualization and analysis of interaction networks

MOTIVATION: Analyzing the networks of interactions between genes and proteins has become a central theme in systems biology. Versatile software tools for interactively displaying and analyzing these networks are therefore very much in demand. The public-domain open software environment Cytoscape has been developed with the goal of facilitating the design and development of such software tools by the scientific community. RESULTS: We present GenePro, a plugin to Cytoscape featuring a set of versatile tools that greatly facilitates the visualization and analysis of protein networks derived from high-throughput interactions data and the validation of various methods for parsing these networks into meaningful functional modules. AVAILABILITY: The GenePro plugin is available at the website http://genepro.ccb.sickkids.ca.     

The antibody mining toolbox

In vitro selection has been an essential tool in the development of recombinant antibodies against various antigen targets. Deep sequencing has recently been gaining ground as an alternative and valuable method to analyze such antibody selections. The analysis provides a novel and extremely detailed view of selected antibody populations, and allows the identification of specific antibodies using only sequencing data, potentially eliminating the need for expensive and laborious low-throughput screening methods such as enzyme-linked immunosorbant assay. The high cost and the need for bioinformatics experts and powerful computer clusters, however, have limited the general use of deep sequencing in antibody selections. Here, we describe the AbMining ToolBox, an open source software package for the straightforward analysis of antibody libraries sequenced by the three main next generation sequencing platforms (454, Ion Torrent, MiSeq). The ToolBox is able to identify heavy chain CDR3s as effectively as more computationally intense software, and can be easily adapted to analyze other portions of antibody variable genes, as well as the selection outputs of libraries based on different scaffolds. The software runs on all common operating systems (Microsoft Windows, Mac OS X, Linux), on standard personal computers, and sequence analysis of 1–2 million reads can be accomplished in 10–15 min, a fraction of the time of competing software. Use of the ToolBox will allow the average researcher to incorporate deep sequence analysis into routine selections from antibody display libraries.     

New programs: XELE—a polypeptide model-building program for a graphics workstation

A model-building program, XELE, for use in protein crystallography has been written in C under UNIX on a graphics workstation. This program makes full use of the X Window system to display the electron density distribution and to manipulate the polypeptide model, and therefore is named XELE. It utilizes a fast three-dimensional rendering package, Dorè, and is portable to other types of graphics workstations. A part of the program for the man-machine interface uses the library of X Window and X Toolkit, and therefore is highly interactive. The structure analysis program package, PROTEIN, is also implemented in an interactive mode using X Window, and has been interfaced with XELE.     

The antibody mining toolbox: An open source tool for the rapid analysis of antibody repertoires

In vitro selection has been an essential tool in the development of recombinant antibodies against various antigen targets. Deep sequencing has recently been gaining ground as an alternative and valuable method to analyze such antibody selections. The analysis provides a novel and extremely detailed view of selected antibody populations, and allows the identification of specific antibodies using only sequencing data, potentially eliminating the need for expensive and laborious low-throughput screening methods such as enzyme-linked immunosorbant assay. The high cost and the need for bioinformatics experts and powerful computer clusters, however, have limited the general use of deep sequencing in antibody selections. Here, we describe the AbMining ToolBox, an open source software package for the straightforward analysis of antibody libraries sequenced by the three main next generation sequencing platforms (454, Ion Torrent, MiSeq). The ToolBox is able to identify heavy chain CDR3s as effectively as more computationally intense software, and can be easily adapted to analyze other portions of antibody variable genes, as well as the selection outputs of libraries based on different scaffolds. The software runs on all common operating systems (Microsoft Windows, Mac OS X, Linux), on standard personal computers, and sequence analysis of 1–2 million reads can be accomplished in 10–15 min, a fraction of the time of competing software. Use of the ToolBox will allow the average researcher to incorporate deep sequence analysis into routine selections from antibody display libraries.     

CyNetworkBMA: a Cytoscape app for inferring gene regulatory networks

Background

Inference of gene networks from expression data is an important problem in computational biology. Many algorithms have been proposed for solving the problem efficiently. However, many of the available implementations are programming libraries that require users to write code, which limits their accessibility.

Results

We have developed a tool called CyNetworkBMA for inferring gene networks from expression data that integrates with Cytoscape. Our application offers a graphical user interface for networkBMA, an efficient implementation of Bayesian Model Averaging methods for network construction. The client-server architecture of CyNetworkBMA makes it possible to distribute or centralize computation depending on user needs.

Conclusions

CyNetworkBMA is an easy-to-use tool that makes network inference accessible to non-programmers through seamless integration with Cytoscape. CyNetworkBMA is available on the Cytoscape App Store at http://apps.cytoscape.org/apps/cynetworkbma.

     

DeepMIB: User-friendly and open-source software for training of deep learning network for biological image segmentation

We present DeepMIB, a new software package that is capable of training convolutional neural networks for segmentation of multidimensional microscopy datasets on any workstation. We demonstrate its successful application for segmentation of 2D and 3D electron and multicolor light microscopy datasets with isotropic and anisotropic voxels. We distribute DeepMIB as both an open-source multi-platform Matlab code and as compiled standalone application for Windows, MacOS and Linux. It comes in a single package that is simple to install and use as it does not require knowledge of programming. DeepMIB is suitable for everyone interested of bringing a power of deep learning into own image segmentation workflows.     

Making more sense of the order: A review of Canoco for Windows 4.5, PC‐ORD version 4 and SYN‐TAX 2000

Abstract. Personal computers of ever‐increasing speed have motivated programmers of multivariate software to adapt their programs to be run in Microsoft Windows and Macintosh platforms. Updated versions of these multivariate programs appear more and more frequently and are marketed intensively. In this review we provide a comparative analysis of the most recent versions of three analytical software packages –Canoco for Windows 4.5, PC‐ORD version 4 and SYN‐TAX 2000. The three packages share two characteristics. First, the most recent versions are now compatible with the most recent Windows platforms and should therefore be accessible for use by virtually all vegetation scientists. Second, they have capabilities for numerous multivariate techniques, although each package has some unique techniques. Thus, any one of the packages will have much to offer the user.     

STARS: statistics on inter-atomic distances and torsion angles in protein secondary structures

SUMMARY: A graphics package has been developed for performing statistics on interatomic distances and torsion angles in protein secondary structures (STARS) from a protein crystal structure database. It allows one to obtain both the graphical view and the text format of distributions of the distances and angles for atoms located in 10 types of protein secondary structures. STARS will facilitate assignment of ambiguous NOESY peaks, structure determination by nuclear magnetic resonance, structure validation and comparison of protein folds. AVAILABILITY: All data, documents and execute files are freely downloadable at http://stars.zhengyuhome.com. The software works appropriately on Windows system, without any compilation or installation. CONTACT: dbsydw@nus.edu.sg.     

Genview and Gencode : a pair of programs to test theories of genetic code evolution

GENVIEW: and GENCODE: are tools for testing the adaptive nature of a genetic code under different assumptions about patterns of genetic error and the nature of amino acid similarity. GENVIEW: provides a user friendly, point-and-click interface by which a user may reproduce and extend analysis of the adaptive properties of the standard genetic code or any of its secondary derivatives. GENVIEW: is a graphical user interface (GUI) program which runs on Linux, Unix and Microsoft Windows platforms and is based on the GTKf + toolkit. GENVIEW: outputs ASCII configuration files which are interpreted by GENCODE: to perform an analysis. GENCODE: is available for the same platforms as GENVIEW.