UCSF ChimeraX is the next-generation interactive visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. ChimeraX brings (a) significant performance and graphics enhancements; (b) new implementations of Chimera's most highly used tools, many with further improvements; (c) several entirely new analysis features; (d) support for new areas such as virtual reality, light-sheet microscopy, and medical imaging data; (e) major ease-of-use advances, including toolbars with icons to perform actions with a single click, basic "undo" capabilities, and more logical and consistent commands; and (f) an app store for researchers to contribute new tools. ChimeraX includes full user documentation and is free for noncommercial use, with downloads available for Windows, Linux, and macOS from https://www.rbvi.ucsf.edu/chimerax.

UCSF ChimeraX: Structure visualization for researchers, educators, and developers.

HMMER is a software suite for protein sequence similarity searches using probabilistic methods Previously, HMMER has mainly been available only as a computationally intensive UNIX command-line tool, restricting its use Recent advances in the software, HMMER3, have resulted in a 100-fold speed gain relative to previous versions It is now feasible to make efficient profile hidden Markov model (profile HMM) searches via the web A HMMER web server (http://hmmerjaneliaorg) has been designed and implemented such that most protein database searches return within a few seconds Methods are available for searching either a single protein sequence, multiple protein sequence alignment or profile HMM against a target sequence database, and for searching a protein sequence against Pfam The web server is designed to cater to a range of different user expertise and accepts batch uploading of multiple queries at once All search methods are also available as RESTful web services, thereby allowing them to be readily integrated as remotely executed tasks in locally scripted workflows We have focused on minimizing search times and the ability to rapidly display tabular results, regardless of the number of matches found, developing graphical summaries of the search results to provide quick, intuitive appraisement of them

/pdf/hmmer-web-server-interactive-sequence-similarity-searching-yikq68wn9e.pdf

HMMER web server: interactive sequence similarity searching

UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This article highlights some specific advances in the areas of visualization and usability, performance, and extensibility. ChimeraX is free for noncommercial use and is available from http://www.rbvi.ucsf.edu/chimerax/ for Windows, Mac, and Linux.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/pro.3235

UCSF ChimeraX: Meeting modern challenges in visualization and analysis.

The EMBL-EBI provides access to various mainstream sequence analysis applications. These include sequence similarity search services such as BLAST, FASTA, InterProScan and multiple sequence alignment tools such as ClustalW, T-Coffee and MUSCLE. Through the sequence similarity search services, the users can search mainstream sequence databases such as EMBL-Bank and UniProt, and more than 2000 completed genomes and proteomes. We present here a new framework aimed at both novice as well as expert users that exposes novel methods of obtaining annotations and visualizing sequence analysis results through one uniform and consistent interface. These services are available over the web and via Web Services interfaces for users who require systematic access or want to interface with customized pipe-lines and workflows using common programming languages. The framework features novel result visualizations and integration of domain and functional predictions for protein database searches. It is available at http://www.ebi.ac.uk/Tools/sss for sequence similarity searches and at http://www.ebi.ac.uk/Tools/msa for multiple sequence alignments.

/pdf/a-new-bioinformatics-analysis-tools-framework-at-embl-ebi-bunw51fdfd.pdf

A new bioinformatics analysis tools framework at EMBL–EBI

Since 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis tools via Web Services interfaces. This comprises services to search across the databases available from the EMBL-EBI and to explore the network of cross-references present in the data (e.g. EB-eye), services to retrieve entry data in various data formats and to access the data in specific fields (e.g. dbfetch), and analysis tool services, for example, sequence similarity search (e.g. FASTA and NCBI BLAST), multiple sequence alignment (e.g. Clustal Omega and MUSCLE), pairwise sequence alignment and protein functional analysis (e.g. InterProScan and Phobius). The REST/SOAP Web Services (http://www.ebi.ac.uk/Tools/webservices/) interfaces to these databases and tools allow their integration into other tools, applications, web sites, pipeline processes and analytical workflows. To get users started using the Web Services, sample clients are provided covering a range of programming languages and popular Web Service tool kits, and a brief guide to Web Services technologies, including a set of tutorials, is available for those wishing to learn more and develop their own clients. Users of the Web Services are informed of improvements and updates via a range of methods.

Analysis Tool Web Services from the EMBL-EBI

The use of Web Services to enable programmatic access to on-line bioinformatics is becoming increasingly important in the Life Sciences. However, their number, distribution and the variable quality of their documentation can make their discovery and subsequent use difficult. A Web Services registry with information on available services will help to bring together service providers and their users. The BioCatalogue (http://www.biocatalogue.org/) provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Services in the BioCatalogue can be described and searched in multiple ways based upon their technical types, bioinformatics categories, user tags, service providers or data inputs and outputs. They are also subject to constant monitoring, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. The system is accessible via a human-readable 'Web 2.0'-style interface and a programmatic Web Service interface. The BioCatalogue follows a community approach in which all services can be registered, browsed and incrementally documented with annotations by any member of the scientific community.

/pdf/biocatalogue-a-universal-catalogue-of-web-services-for-the-47t9hkdqdr.pdf

BioCatalogue: a universal catalogue of web services for the life sciences

Web Services have gained a momentum as a means for packaging existing data and computational resources in a form that is amenable for use and composition by third party applications. The life science community is certainly among the first adopters of Web Services. For example, "Taverna":http://www.mygrid.org.uk, a workflow workbench that is popular within the life science community, provides access to over 3500 thousands web services that can be composed by scientists for constructing and enacting their in silico experiments. However, one of the main issues that hinders the wide adoption and use of Web Services is the difficulty in locating the “appropriate” Web Service, i.e., the Web Service that performs the analysis the scientist is interested in. The descriptions of available Web Services are often poor providing little information to the scientist about their usefulness for the analysis s/he is after. With the above issues in mind, the authors have recently initiated the BioCatalogue project ("http://www.biocatalogue.org/":http://www.biocatalogue.org/). BioCatalogue provides a central registry of curated biological Web Services. A place where providers, users and expert curators can register, annotate and search for Web Services. It also acts as a place where the community can contact and meet the experts and maintainers of these services. The project is co-developed by the University of Manchester and the EMBL-EBI.

BioCatalogue: A Curated Web Service Registry For The Life Science Community

Web services have gained a momentum as a means for packaging existing data and computational resources in a form that is amenable for use and composition by third party applications. They provide a well defined programming interface to integrate tools into applications over networks. Software applications written in various programming languages and running on various platforms can use web services to exchange data over the Internet. The life science community is certainly among the first adopters of web services.

{BioCatalogue}: A Curated Web Service Registry for the Life Science Community

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BioCatalogue: a universal catalogue of web services for the life sciences

BioCatalogue: A Curated Web Service Registry For The Life Science Community

{BioCatalogue}: A Curated Web Service Registry for the Life Science Community