PROSOFT: A general purpose software in protein chemistry

Applesoft and 6502 Assembler software was designed to quicklyperform operations commonly encountered in protein chemistry.It was not designed for a specific application but can be convenientlyused to speed up the determination of protein primary structure. Received on October 6, 1987; accepted on November 10, 1987     

OntoVisT: A general purpose Ontological Visualization Tool

Ontologies have emerged as a fast growing research topic in the area of semantic web during last decade. Currently there are 204 ontologies that are available through OBO Foundry and BioPortal. Several excellent tools for navigating the ontological structure are available, however most of them are dedicated to a specific annotation data or integrated with specific analysis applications, and do not offer flexibility in terms of general-purpose usage for ontology exploration. We developed OntoVisT, a web based ontological visualization tool. This application is designed for interactive visualization of any ontological hierarchy for a specific node of interest, up to the chosen level of children and/or ancestor. It takes any ontology file in OBO format as input and generates output as DAG hierarchical graph for the chosen query. To enhance the navigation capabilities of complex networks, we have embedded several features such as search criteria, zoom in/out, center focus, nearest neighbor highlights and mouse hover events. The application has been tested on all 72 data sets available in OBO format through OBO foundry. The results for few of them can be accessed through OntoVisT-Gallery. AVAILABILITY: The database is available for free at http://ccbb.jnu.ac.in/OntoVisT.html.     

A general purpose computer analysis system for chromatographic data

A manual integration system for the analysis of chromatographicdata is described. The analog output produced by an HPLC absorbancemonitor is passed to a non-inverting signal amplifier. Thisamplified signal is sent to an IBM PC where an analog to digitalconverter is used to digitize the data. A set of six computerprograms which collect, store and analyze these data are presented.This system was used to analyze the nucleotide content of theanaerobic organism Clostridium aceto-butylicum by strong anion-exchangeHPLC. Received on May 26, 1987; accepted on November 15, 1987     

A general purpose method for extracting RNA from Dictyostelium cells

Here we present a protocol for the extraction of RNA from Dictyostelium discoideum. Dictyostelium is a social amoeba that undergoes a basic developmental program, and therefore analysis of RNA levels over a time course is a commonly used technique. This procedure is similar to other guanidine thiocyanate-based methods; however, it has been adjusted because of the large quantities of carbohydrate and nucleases found in Dictyostelium cells. After cell lysis and phenol:chloroform extraction, the resulting high-quality RNA isolated with the described protocol allows the molecular genetic analysis of wild-type and genetically modified cells. The purified RNA can be used for analyses such as northern blotting, RT-PCR and microarrays. This procedure requires approximately 2 h to complete.     

A general purpose genotype in an ancient asexual

Many parthenogenetic species are geographically more widely distributed than their sexual relatives. Their success has been partly attributed to the existence of general purpose genotypes (GPGs). Darwinula stevensoni is an ostracod species, which has persisted for >25 million years without sex, and is both ubiquitous and cosmopolitan. Here, we test the hypothesis that this ancient asexual species may possess a highly generalised (or general purpose) genotype. The ecological tolerance of D. stevensoni was compared with asexual populations of Heterocypris incongruens, a common cypridinid species with mixed reproduction, as well as with that of another ancient asexual darwinulid species with a limited geographic and ecological distribution, Vestalenula molopoensis. The unusually wide tolerance range for both salinity (0-30 g/l) and temperature (10°C, 20°C and 30°C) of the freshwater species D. stevensoni, supports the hypothesis that this ancient asexual has indeed developed a GPG. This coincides with its wide geographic and ecological distribution and might explain its persistence as an obligate asexual in its long-term evolution. The more restricted salinity tolerance of V. molopoensis (maximum at 12 g/l) shows that not all species of the ancient asexual family Darwinulidae have a GPG. D. stevensoni has a much broader tolerance than the asexuals of H. incongruens. We argue why a GPG is most likely to develop in long-term asexuals.     

A reliable general purpose method for extracting genomic DNA from Dictyostelium cells

In this protocol, we present a standard method for extracting DNA from cells of the social amoeba Dictyostelium discoideum. While this procedure is similar to other phenol:chloroform-based purification methods, it is modified to account for the high level of carbohydrate and nucleases found in Dictyostelium cells. Genomic DNA can be isolated from wild-type and genetically modified cells using the described protocol, allowing molecular genetic analyses to be performed. Following cell lysis, nucleic acid extraction, and precipitation, the isolated DNA is suitable for digestion by restriction enzymes, amplification by PCR and Southern blotting. This procedure takes approximately 3 h to complete.     

CR3: a general purpose adhesion-recognition receptor essential for innate immunity

CR3 (CD11b/CD18), a beta(2) integrin, has a key role in innate antimicrobial defenses, as evidenced by the leukocyte adhesion (CD18) deficiency syndrome in humans and the CD11b knockout mouse. CR3 is a highly versatile pattern-recognition receptor that activates leukocytes via signaling complexes and actin reorganization, mediates phagocytosis, and promotes leukocyte transmigration.     

A general purpose non-linear curve fitting program for the British Broadcasting Corporation Microcomputer

Software for non–linear curve fitting has been writtenin BASIC to execute on the British Broadcasting CorporationMicrocomputer. The program uses the direct search algorithmPattern–search, a robust algorithm that has the additionaladvantage of needing specification of the Junction without inclusionof the partial derivatives. Although less efficient than gradientmethods, the program can be readily configured to solve low–dimensionaloptimization problems that are normally encountered in lifesciences. In writing the software, emphasis has been placedupon the ‘user interface’ and making the most efficientuse of the facilities provided by the minimal configurationof this system. Received on March 4, 1985; accepted on March 14, 1985     

合成生物学基因设计软件:iGEM设计综述

随着基因回路规模的扩大,和应用范围的拓展,传统的合成基因回路的设计思路面临着新的挑战。新合成基因回路构建的试验周期长,试错成本大,单纯依靠经验进行设计构建,难以迅速得到满意的结果。iGEM中软件设计比赛旨在帮助合成生物学家,更高效地完成基因回路的设计与预测。为了更好地研究iGEM软件的设计与研究方向,寻找新的设计思路和理念,综述了最近几年iGEM软件队的项目,仔细总结了每一个项目的背景、目的,设计和应用。通过对比和总结,发现这几年的iGEM软件项目从功能上可以分为以下四类:①辅助设计;②资料共享;③合作交流;④数据分析。该综述可以为今后iGEM软件设计提供思考方向,也为合成生物学的发展提供新的思路。     

A general purpose parallel block structured open source incompressible flow solver

A general purpose incompressible flow solver, called caffa3d.MBRi, is presented which features a block structured framework to accommodate both a flexible approach to geometry representation and a straightforward implementation of parallel capabilities through the MPI library. Representation of complex geometries can be handled semi automatically through a combination of body fitted blocks of grids and the immersed boundary condition strategy over both Cartesian and body fitted grid blocks. The parallelization strategy is based on the same block structured framework, by means of encapsulated MPI calls performing a set of conceptually defined high level communication tasks. A set of real world applications ranging from bioengineering to microclimate scenarios is presented to demonstrate the capabilities of the solver, which is open source and freely available through the web page.     

A general purpose computerized display and analysis system for image processing in nuclear medicine.

In this work a general purpose image processor is described, which takes into account the special features and the various requirements for analysing images in nuclear medicine. A new approach for system structure involving encoding and representing medical images is given. This encoder, which is part of the image processor, is efficient especially for long-term storage and for certain pattern recognition in medical imaging. In this processor a statistical package is incorporated for collecting medical statistics using the acquired patient data. This information is used together with the encoder for an automated diagnostic system.     

TFLUX: a general purpose program for the interpretation of radioactive tracer experiments.

TFLUX is a computer program which simulates radioactive tracer experiments using intact cells under steady-state conditions. It is designed for the naive computer user to use, providing English-like input. An example is described in which compartmentation and flux through the citric acid cycle in Dictyostelium discoideum are simulated.     

A federated design for a neurobiological simulation engine: the CBI federated software architecture

Simulator interoperability and extensibility has become a growing requirement in computational biology. To address this, we have developed a federated software architecture. It is federated by its union of independent disparate systems under a single cohesive view, provides interoperability through its capability to communicate, execute programs, or transfer data among different independent applications, and supports extensibility by enabling simulator expansion or enhancement without the need for major changes to system infrastructure. Historically, simulator interoperability has relied on development of declarative markup languages such as the neuron modeling language NeuroML, while simulator extension typically occurred through modification of existing functionality. The software architecture we describe here allows for both these approaches. However, it is designed to support alternative paradigms of interoperability and extensibility through the provision of logical relationships and defined application programming interfaces. They allow any appropriately configured component or software application to be incorporated into a simulator. The architecture defines independent functional modules that run stand-alone. They are arranged in logical layers that naturally correspond to the occurrence of high-level data (biological concepts) versus low-level data (numerical values) and distinguish data from control functions. The modular nature of the architecture and its independence from a given technology facilitates communication about similar concepts and functions for both users and developers. It provides several advantages for multiple independent contributions to software development. Importantly, these include: (1) Reduction in complexity of individual simulator components when compared to the complexity of a complete simulator, (2) Documentation of individual components in terms of their inputs and outputs, (3) Easy removal or replacement of unnecessary or obsoleted components, (4) Stand-alone testing of components, and (5) Clear delineation of the development scope of new components.