SciCombinator

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

Concept: Web server

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

157

Protein-coding genes with multiple alternative polyadenylation sites can generate mRNA 3'UTR sequences of different lengths, thereby causing the loss or gain of regulatory elements, which can affect stability, localization and translation efficiency. 3USS is a web-server developed with the aim of giving experimentalists the possibility to automatically identify alternative 3'UTRs (shorter or longer with respect to a reference transcriptome), an option that is not available in standard RNA-seq data analysis procedures. The tool reports as putative novel the 3'UTRs not annotated in available databases. Furthermore, if data from two related samples are uploaded, common and specific alternative 3'UTRs are identified and reported by the server. Availability: 3USS is freely available at http://www.biocomputing.it/3uss_server.

Concepts: DNA, Gene expression, RNA, Messenger RNA, Computer, Polyadenylation, Three prime untranslated region, Web server

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

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

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

7

Semantic Web technologies have been widely applied in the life sciences, for example by data providers such as OpenLifeData and through web services frameworks such as SADI. The recently reported OpenLifeData2SADI project offers access to the vast OpenLifeData data store through SADI services.

Concepts: Scientific method, Science, Semantic Web, Web 2.0, Internet, Web services, Web server, Web service

6

Hadoop MapReduce-based approaches have become increasingly popular due to their scalability in processing large sequencing data sets. However, as these methods typically require in-depth expertise in Hadoop and Java, they are still out of reach of many bioinformaticians. In order to solve this problem, we have created SeqPig, a library and a collection of tools to manipulate, analyze and query sequencing data sets in a scalable and simple manner. SeqPig scripts use the Hadoop-based distributed scripting engine Apache Pig, which automatically parallelizes and distributes data processing tasks. We demonstrate SeqPig’s scalability over many computing nodes and illustrate its use with example scripts.Availability and Implementation: Available under the open source MIT license at http://sourceforge.net/projects/seqpig/ CONTACT: andre.schumacher@yahoo.com SUPPLEMENTARY INFORMATION: Instructions and examples for SeqPig.

Concepts: PHP, JavaScript, Web server, Python, Scripting language, Lua, MIT License, JQuery

5

We present an update to our Galaxy-based web server for processing and visualizing deeply sequenced data. Its core tool set, deepTools, allows users to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches. Since we first described our deepTools Galaxy server in 2014, we have implemented new solutions for many requests from the community and our users. Here, we introduce significant enhancements and new tools to further improve data visualization and interpretation. deepTools continue to be open to all users and freely available as a web service atdeeptools.ie-freiburg.mpg.de The new deepTools2 suite can be easily deployed within any Galaxy framework via the toolshed repository, and we also provide source code for command line usage under Linux and Mac OS X. A public and documented API for access to deepTools functionality is also available.

Concepts: Java, Mac OS X, Operating system, Mac OS, Macintosh, Graphical user interface, Linux, Web server

3

We describe a novel freely available web server Base of Bioisosterically Exchangeable Replacements (BoBER), which implements an interface to a database of bioisosteric and scaffold hopping replacements. Bioisosterism and scaffold hopping are key concepts in drug design and optimization, and can be defined as replacements of biologically active compound’s fragments with other fragments to improve activity, reduce toxicity, change bioavailability or to diversify the scaffold space. Our web server enables fast and user-friendly searches for bioisosteric and scaffold replacements which were obtained by mining the whole Protein Data Bank. The working of the web server is presented on an existing MurF inhibitor as example. BoBER web server enables medicinal chemists to quickly search for and get new and unique ideas about possible bioisosteric or scaffold hopping replacements that could be used to improve hit or lead drug-like compounds.

Concepts: Java, Medicinal chemistry, World Wide Web, Internet, Protein Data Bank, User interface, Web page, Web server