The BioTools Suite

The BioTools Suite is a set of three comprehensive, platform-independent software packages (PepTool, GeneTool, and ChromaTool) developed for sequence assembly and analysis. In addition to supporting a large number of standard bioinformatics functions, these programs also incorporate a number of useful innovations including uniform graphical-user interface (GUI) design, direct internet connectivity, a novel approach to feature annotation, and a variety of enhanced algorithms for large scale proteome and genome analysis. This article describes the key features, recent changes, and general operation of all three programs.     

Operative Colonoscopy

In 12 patients with radiologically-proved lesions of the colon total retrograde fibreoptic colonoscopy was performed on the unopened bowel at laparotomy. Additional polyps were found in five patients, and in four of these the polyp was not readily palpable through the bowel wall. This procedure is indicated whenever there are reasonable grounds for suspecting the presence of multiple polypi.     

GEDAS - Gene Expression Data Analysis Suite

Currently available micro-array gene expression data analysis tools lack standardization at various levels. We developed GEDAS (gene expression data analysis suite) to bring various tools and techniques in one system. It also provides a number of other features such as a large collection of distance measures and pre-processing techniques. The software is an extension of Cluster 3.0 (developed based on Eisen Lab's Cluster and Tree View software). GEDAS allows the usage of different datasets with algorithms such as k-means, HC, SVD/PCA and SVM, in addition to Kohonen's SOM and LVQ.

Availability     

A Suite of Adaptations for Intertidal Spawning

Salt marshes and similar tide-dominated habitats present anunusual challenge for reproduction of resident aquatic organisms.Strong currents, siltation and hypoxia can potentially contributeto reproductive failure through mortality of the eggs or flushingof the eggs and larvae from the habitat. Fundulus heteroclitus,a small brackish water killifish, is a common resident of tidalmarshes along the east coast of North America from Newfoundlandto Florida. The reproductive strategy of this and related speciesis based on aerial incubation of eggs in the high intertidalzone. The eggs are resistant to desiccation and, when fullydeveloped, hatch on immersion. Copulatory behavior and anatomyof accessory reproductive structures are adapted to placementof eggs in protected incubation sites. The gonads of both malesand females mature rhythmically with an endogenous circasemilunarperiod, which is synchronized with the "spring" tides of newand full moons. Spawning occurs on high tides. Embryos developin 9–15 days, and usually hatch on the succeeding springtide series. Reproductive cyclicity in F. heteroclitus and relatedfishes ensures that spawning fish will have access to the highintertidal zone, thereby permitting aerial incubation of eggs.