SciCombinator

Discover the most talked about and latest scientific content & concepts.

Concept: Web page

172

BACKGROUND: A molecule editor, i.e. a program facilitating graphical input and interactive editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. Today, when a web browser has become the universal scientific user interface, a tool to edit molecules directly within the web browser is essential. One of the most popular tools for molecular structure input on the web is the JME applet. Since its release nearly 15 years ago, however the web environment has changed and Java applets are facing increasing implementation hurdles due to their maintenance and support requirements, as well as security issues. This prompted us to update the JME editor and port it to a modern Internet programming language - JavaScript. SUMMARY: The actual molecule editing Java code of the JME editor was translated into JavaScript with help of the Google Web Toolkit compiler and a custom library that emulates a subset of the GUI features of the Java runtime environment. In this process, the editor was enhanced by additional functionalities including a substituent menu, copy/paste, drag and drop and undo/redo capabilities and an integrated help. In addition to desktop computers, the editor supports molecule editing on touch devices, including iPhone, iPad and Android phones and tablets. In analogy to JME the new editor is named JSME. This new molecule editor is compact, easy to use and easy to incorporate into web pages. CONCLUSIONS: A free molecule editor written in JavaScript was developed and is released under the terms of permissive BSD license. The editor is compatible with JME, has practically the same user interface as well as the web application programming interface. The JSME editor is available for download from the project web page http://peter-ertl.com/jsme/

Concepts: Java, World Wide Web, Programming language, Web browser, Web page, Google, Web server, HTML

154

JBrowse is a fast and full-featured genome browser built with JavaScript and HTML5. It is easily embedded into websites or apps but can also be served as a standalone web page.

Concepts: World Wide Web, Website, Web browser, Web page, Adobe Flash, Netscape, Web server, HTML

149

IsoMIF Finder is an online server for the identification of molecular interaction field (MIF) similarities. User defined binding site MIFs can be compared to datasets of pre-calculated MIFs or against a user-defined list of PDB entries. The interface can be used for the prediction of function, identification of potential cross-reactivity or polypharmacological targets and drug repurposing. Detected similarities can be viewed in a browser or within a PyMOL session.

Concepts: Pharmacology, Molecular biology, Atom, Object-oriented programming, Web page, Binary relation

28

SUMMARY: Cancer is the leading cause of death worldwide. Screening anticancer candidates from tens of millions of chemical compounds is expensive and time-consuming. A rapid and user-friendly web server, known as CDRUG, is described here to predict the anticancer activity of chemical compounds. In CDRUG, a hybrid score was developed to measure the similarity of different compounds. The performance analysis shows that CDRUG has the area under curve (AUC) of 0.878, indicating that CDRUG is effective to distinguish active and inactive compounds. AVAILABILITY: The CDRUG web server and the standard-alone version are freely available at http://bsb.kiz.ac.cn/CDRUG/ CONTACT: huangjf@mail.kiz.ac.cn. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Concepts: Scientific method, Cancer, Chemical element, Integral, Chemical compound, World Wide Web, Web page, Web server

26

We present the Proteomics Identifications and Quantitations Data Management and Integration Service or PIQMIe that aids in reliable and scalable data management, analysis and visualization of semi-quantitative mass spectrometry based proteomics experiments. PIQMIe readily integrates peptide and (non-redundant) protein identifications and quantitations from multiple experiments with additional biological information on the protein entries, and makes the linked data available in the form of a light-weight relational database, which enables dedicated data analyses (e.g. in R) and user-driven queries. Using the web interface, users are presented with a concise summary of their proteomics experiments in numerical and graphical forms, as well as with a searchable protein grid and interactive visualization tools to aid in the rapid assessment of the experiments and in the identification of proteins of interest. The web server not only provides data access through a web interface but also supports programmatic access through RESTful web service. The web server is available at http://piqmie.semiqprot-emc.cloudlet.sara.nl or http://www.bioinformatics.nl/piqmie. This website is free and open to all users and there is no login requirement.

Concepts: Protein, Peptide, World Wide Web, Internet, Hypertext Transfer Protocol, Web page, Web server, Web api

24

PRO: tein S: tructure A: nnotation T: ool-plus (ProSAT(+)) is a new web server for mapping protein sequence annotations onto a protein structure and visualizing them simultaneously with the structure. ProSAT(+) incorporates many of the features of the preceding ProSAT and ProSAT2 tools but also provides new options for the visualization and sharing of protein annotations. Data are extracted from the UniProt KnowledgeBase, the RCSB PDB and the PDBe SIFTS resource, and visualization is performed using JSmol. User-defined sequence annotations can be added directly to the URL, thus enabling visualization and easy data sharing. ProSAT(+) is available at http://prosat.h-its.org.

Concepts: Protein, Protein structure, Primary structure, UniProt, Computer, World Wide Web, Protein Data Bank, Web page

24

N(6)-methyladenosine (m(6)A), catalyzed by N(6)-adenosyl methyltransferases, is one of the most abundant RNA modifications and has fundamental regulatory roles in cell. With the avalanche of data generated from biological experiments, it is urgent to develop computational methods for timely and accurately identifying m(6)A sites. In view of this, a web-server called MethyRNA is proposed by formulating RNA sequences with nucleotide chemical property and frequency. In the jackknife cross-validation test, MethyRNA obtained the accuracies of 90.38% and 88.39% for identifying m(6)A sites in Homo sapiens and Mus musculus, indicating that MethyRNA hold the potential to become a useful tool for m(6)A site identification. Additionally, a user-friendly web server for MethyRNA was established at http://lin.uestc.edu.cn/server/methyrna.

Concepts: DNA, Gene, Human, RNA, Chemistry, Computer, Web page, Web server

10

Calypso is an easy-to-use online software suite that allows non-expert users to mine, interpret and compare taxonomic information from metagenomic or 16S rDNA datasets. Calypso has a focus on multivariate statistical approaches that can identify complex environment-microbiome associations. The software enables quantitative visualizations, statistical testing, multivariate analysis, supervised learning, factor analysis, multivariable regression, network analysis and diversity estimates. Comprehensive help pages, tutorials and videos are provided via a wiki page.

Concepts: Scientific method, Regression analysis, Statistics, Sociology, Multivariate statistics, Psychometrics, Factor analysis, Web page

9

Next-generation DNA sequencing technologies have made it possible to generate transcriptome data for novel organisms quickly and cheaply, to the extent that the effort required to annotate and publish a new transcriptome is greater than the effort required to sequence it. Often, following publication, details of the annotation effort are only available in summary form, hindering subsequent exploitation of the data. To promote best-practice in annotation and to ensure that data remain accessible, we have written afterParty, a web application that allows users to assemble, annotate and publish novel transcriptomes using only a web browser.

Concepts: DNA, Molecular biology, Writing, World Wide Web, Publishing, Web browser, Web page, Microsoft

7

Cytoscape.js is an open-source JavaScript-based graph library. Its most common use case is as a visualization software component, so it can be used to render interactive graphs in a web browser. It also can be used in a headless manner, useful for graph operations on a server, such as Node.js.

Concepts: Scientific method, Graph theory, World Wide Web, Web browser, Web page, Graph, Microsoft, Netscape