Photosynthesis and the Web: 2001

First, a brief history of the Internet and the World Wide Web is presented. This is followed by relevant information on photosynthesis-related web sites grouped into several categories: (1) large group sites, (2) comprehensive overview sites, (3) specific subject sites, (4) individual researcher sites, (5) kindergarten through high school (K-12) educational sites, (6) books and journals, and, 7) other useful sites. A section on searching the Web is also included. Finally, we have included an appendix with all of the web sites discussed herein as well as other web sites that space did not allow. Readers are requested to send comments, corrections and additions to gov@uiuc.edu. This revised version was published online in June 2006 with corrections to the Cover Date.     

Web-building behaviour in the orb-weaving spider Zygiella x-notata: influence of experience

Zygiella x-notata is an orb-weaving spider that often renews its trap daily. Web building has associated costs and benefits, and building successive webs may have consequences for lifetime reproductive success. In the laboratory, we tested the ability of Z. x-notata to modify its building behaviour in response to various stages in predation (prey detection, capture and ingestion) experienced with a previous web. We determined which stages provided information for the spiders. Spiders that detected, captured and ingested prey and then rebuilt their web used less silk and made a smaller capture area than in the previous web. There was no effect of prey detection alone on the next web. Capture without feeding gave the same results as capture followed by feeding. The spiders that ate prey without detection and capture (feeding by hand) had the same energetic gains as spiders that caught prey but delayed building a new web. The spiders thus showed plasticity in web-building behaviour and in the amount of silk used (energetic investment) in the short term (from one web to the next). Changes in body condition may therefore influence web construction. Moreover, information gained during prey capture appeared to influence the size and structure of the next web. This ability should enable spiders to adapt their web building to maximize their fitness. Copyright 2000 The Association for the Study of Animal Behaviour.     

Kleptoparasites or commensals? Effects of Argyrodes antipodianus (Araneae: Theridiidae) on Nephila plumipes (Araneae: Tetragnathidae)

Argyrodes antipodianus is a small kleptobiotic spider that steals prey from webs of the large orb-weaving spider Nephila plumipes, and sometimes removes the web itself. We used experiments in a greenhouse to test how the presence of the kleptobiont, differences in food availability, and web damage affected fitness of the web owner. After 49 days, N. plumipes with four A. antipodianus on their webs gained 55% less weight and relocated their webs 4.5 times as often as spiders with no kleptobionts. Increased web relocation and decreased weight gain may have resulted from reduced prey levels or from web damage by A. antipodianus. A second experiment demonstrated that hosts gained weight at the feeding rate used in the first experiment, but not at lower rates. Web relocation rate also varied with feeding rate, but in a non-linear manner. Web loss was evaluated in a separate experiment, by manually removing one-quarter of the web every 5 days for 30 days; however, neither weight gain nor rate of web relocation were affected. We conclude that A. antipodianus is a true kleptoparasite that can reduce the growth rate of its host N. plumipes, but that neither food theft nor web damage alone explain increased web relocation rates. Received: 28 November 1996 / Accepted: 3 April 1997     

Presentation Accuracy of the Web Revisited: Animation Methods in the HTML5 Era

Using the Web to run behavioural and social experiments quickly and efficiently has become increasingly popular in recent years, but there is some controversy about the suitability of using the Web for these objectives. Several studies have analysed the accuracy and precision of different web technologies in order to determine their limitations. This paper updates the extant evidence about presentation accuracy and precision of the Web and extends the study of the accuracy and precision in the presentation of multimedia stimuli to HTML5-based solutions, which were previously untested. The accuracy and precision in the presentation of visual content in classic web technologies is acceptable for use in online experiments, although some results suggest that these technologies should be used with caution in certain circumstances. Declarative animations based on CSS are the best alternative when animation intervals are above 50 milliseconds. The performance of procedural web technologies based on the HTML5 standard is similar to that of previous web technologies. These technologies are being progressively adopted by the scientific community and have promising futures, which makes their use advisable to utilizing more obsolete technologies.     

Guide to the Internet. The world wide web.

The world wide web provides a uniform, user friendly interface to the Internet. Web pages can contain text and pictures and are interconnected by hypertext links. The addresses of web pages are recorded as uniform resource locators (URLs), transmitted by hypertext transfer protocol (HTTP), and written in hypertext markup language (HTML). Programs that allow you to use the web are available for most operating systems. Powerful on line search engines make it relatively easy to find information on the web. Browsing through the web--"net surfing"--is both easy and enjoyable. Contributing to the web is not difficult, and the web opens up new possibilities for electronic publishing and electronic journals.     

GeneCruiser: a web service for the annotation of microarray data

SUMMARY: GeneCruiser is a web service allowing users to annotate their genomic data by mapping microarray feature identifiers to gene identifiers from databases, such as UniGene, while providing links to web resources, such as the UCSC Genome Browser. It relies on a regularly updated database that retrieves and indexes the mappings between microarray probes and genomic databases. Genes are identified using the Life Sciences Identifier standard. AVAILABILITY: GeneCruiser is freely available in the following forms: Web service and Web application, http://www.genecruiser.org; GenePattern, GeneCruiser access has been integrated into our microarray analysis platform, GenePattern. http://www.genepattern.org.     

PRODISTIN Web Site: a tool for the functional classification of proteins from interaction networks

The PRODISTIN Web Site is a web service allowing users to functionally classify genes/proteins from any type of interaction network. The resulting computation provides a classification tree in which (1) genes/proteins are clustered according to the identity of their interaction partners and (2) functional classes are delineated in the tree using the Biological Process Gene Ontology annotations. AVAILABILITY: The PRODISTIN Web Site is freely accessible at http://gin.univ-mrs.fr/webdistin     

A web services choreography scenario for interoperating bioinformatics applications

Background  

Very often genome-wide data analysis requires the interoperation of multiple databases and analytic tools. A large number of genome databases and bioinformatics applications are available through the web, but it is difficult to automate interoperation because: 1) the platforms on which the applications run are heterogeneous, 2) their web interface is not machine-friendly, 3) they use a non-standard format for data input and output, 4) they do not exploit standards to define application interface and message exchange, and 5) existing protocols for remote messaging are often not firewall-friendly. To overcome these issues, web services have emerged as a standard XML-based model for message exchange between heterogeneous applications. Web services engines have been developed to manage the configuration and execution of a web services workflow.     

Convergent evolution of eye ultrastructure and divergent evolution of vision-mediated predatory behaviour in jumping spiders

All jumping spiders have unique, complex eyes with exceptional spatial acuity and some of the most elaborate vision-guided predatory strategies ever documented for any animal of their size. However, it is only recently that phylogenetic techniques have been used to reconstruct the relationships and key evolutionary events within the Salticidae. Here, we used data for 35 species and six genes (4.8 kb) for reconstructing the phylogenetic relationships between Spartaeinae, Lyssomaninae and Salticoida. We document a remarkable case of morphological convergence of eye ultrastructure in two clades with divergent predatory behaviour. We, furthermore, find evidence for a stepwise, gradual evolution of a complex predatory strategy. Divergent predatory behaviour ranges from cursorial hunting to building prey-catching webs and araneophagy with web invasion and aggressive mimicry. Web invasion and aggressive mimicry evolved once from an ancestral spartaeine that was already araneophagic and had no difficulty entering webs due to glue immunity. Web invasion and aggressive mimicry was lost once, in Paracyrba, which has replaced one highly specialized predation strategy with another (hunting mosquitoes). In contrast to the evolution of divergent behaviour, eyes with similarly high spatial acuity and ultrastructural design evolved convergently in the Salticoida and in Portia.     

Mfold web server for nucleic acid folding and hybridization prediction

The abbreviated name, 'mfold web server', describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large. By making use of universally available web GUIs (Graphical User Interfaces), the server circumvents the problem of portability of this software. Detailed output, in the form of structure plots with or without reliability information, single strand frequency plots and 'energy dot plots', are available for the folding of single sequences. A variety of 'bulk' servers give less information, but in a shorter time and for up to hundreds of sequences at once. The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/mfold. This URL will be referred to as 'MFOLDROOT'.     

Biological SOAP servers and web services provided by the public sequence data bank

A number of biological data resources (i.e. databases and data analytical tools) are searchable and usable on-line thanks to the internet and the World Wide Web (WWW) servers. The output from the web server is easy for us to browse. However, it is laborious and sometimes impossible for us to write a computer program that finds a useful data resource, sends a proper query and processes the output. It is a serious obstacle to the integration of distributed heterogeneous data resources. To solve the issue, we have implemented a SOAP (Simple Object Access Protocol) server and web services that provide a program-friendly interface. The web services are accessible at http://www.xml.nig.ac.jp/.     

EntrezAJAX: direct web browser access to the Entrez Programming Utilities

Web applications for biology and medicine often need to integrate data from Entrez services provided by the National Center for Biotechnology Information. However, direct access to Entrez from a web browser is not possible due to 'same-origin' security restrictions. The use of "Asynchronous JavaScript and XML" (AJAX) to create rich, interactive web applications is now commonplace. The ability to access Entrez via AJAX would be advantageous in the creation of integrated biomedical web resources. We describe EntrezAJAX, which provides access to Entrez eUtils and is able to circumvent same-origin browser restrictions. EntrezAJAX is easily implemented by JavaScript developers and provides identical functionality as Entrez eUtils as well as enhanced functionality to ease development. We provide easy-to-understand developer examples written in JavaScript to illustrate potential uses of this service. For the purposes of speed, reliability and scalability, EntrezAJAX has been deployed on Google App Engine, a freely available cloud service. The EntrezAJAX webpage is located at     

Effect of abiotic factors on the foraging strategy of the orb‐web spider Argiope keyserlingi (Araneae: Araneidae)

Abstract Environmental conditions such as light level, background contrast and temperature might influence a spider's prey capture success and risk of predation. Thus it may often be advantageous for spiders to adjust web‐building behaviour in response to variation in these environmental conditions. This hypothesis was examined in a study of the construction of webs and web decorations (conspicuous strands of silk at the hub of the web) of the orb‐web spider Argiope keyserlingi. Web decorations are thought to have one or more separate functions. They may attract prey, deter predators or advertise the web to oncoming birds, thus preventing web damage. In this series of experiments, relationships between weather parameters and the construction of webs and web decorations were considered. In complementary laboratory experiments, A. keyserlingi spiders were exposed to two different light levels (700 and 90 lx), background contrasts (black and white) and temperature conditions (20 and 26°C). Of the available weather parameters, only temperature was significantly related to web decorating behaviour but not to web size. In the laboratory, temperature also influenced web‐decorating behaviour, and spiders in dim light (700 lx) constructed larger webs and longer decorations. Background contrast did not significantly alter web size or web decorations. These data suggest that when prey availability is reduced at low temperatures, spiders may use web decorations to attract prey to the web. Similarly, in dim light, spiders may build more and larger decorations to increase the visual signal to approaching prey or to advertise the web to oncoming birds.     

Web Queries as a Source for Syndromic Surveillance

In the field of syndromic surveillance, various sources are exploited for outbreak detection, monitoring and prediction. This paper describes a study on queries submitted to a medical web site, with influenza as a case study. The hypothesis of the work was that queries on influenza and influenza-like illness would provide a basis for the estimation of the timing of the peak and the intensity of the yearly influenza outbreaks that would be as good as the existing laboratory and sentinel surveillance. We calculated the occurrence of various queries related to influenza from search logs submitted to a Swedish medical web site for two influenza seasons. These figures were subsequently used to generate two models, one to estimate the number of laboratory verified influenza cases and one to estimate the proportion of patients with influenza-like illness reported by selected General Practitioners in Sweden. We applied an approach designed for highly correlated data, partial least squares regression. In our work, we found that certain web queries on influenza follow the same pattern as that obtained by the two other surveillance systems for influenza epidemics, and that they have equal power for the estimation of the influenza burden in society. Web queries give a unique access to ill individuals who are not (yet) seeking care. This paper shows the potential of web queries as an accurate, cheap and labour extensive source for syndromic surveillance.     

A Web Interface for Easy Flexible Protein-Protein Docking with ATTRACT

Protein-protein docking programs can give valuable insights into the structure of protein complexes in the absence of an experimental complex structure. Web interfaces can facilitate the use of docking programs by structural biologists. Here, we present an easy web interface for protein-protein docking with the ATTRACT program. While aimed at nonexpert users, the web interface still covers a considerable range of docking applications. The web interface supports systematic rigid-body protein docking with the ATTRACT coarse-grained force field, as well as various kinds of protein flexibility. The execution of a docking protocol takes up to a few hours on a standard desktop computer.