products New Products Geneious Server
Geneious Server, the next-generation sequencing (NGS) analysis package from Biomatters, has added several new algorithms and improved capabilities to facilitate the offl oading of high-intensity processing to computer clusters directly from researchers’ desktops. Combined with the Geneious Pro desktop software, users will have a wider choice of algorithms and direct access to the full power of their institution’s computing grid or cluster. The LastZ, Glimmer, PAUP* and
Origin and OriginPro 8.5.1
OriginLab has announced the release of Origin 8.5.1 and OriginPro 8.5.1. Improvements to previous versions include two new data analysis Gadgets, namely Cluster Gadget and Quick Peaks Gadget, and a versatile tool for reconstructing a graph from a scanned image. Originally introduced in Origin 8.5, Gadgets provide an intuitive interface for performing dynamic data analysis on a selected region of data. The Quick Peaks Gadget allows the user to defi ne and subtract a baseline from spectra and identify peak locations within a region of interest. Support is provided to output over 15 peak parameters, including peak location in x/y, area, and centroid. Available in OriginPro, a ‘Fit Peaks’ context menu allows users to fi t the identifi ed peaks by selecting from more than 20 built-in peak functions, or a user-defi ned peak function.
www.originlab.com/Origin851
SOAP2 algorithms can now be launched from a desktop to run on Geneious Server or be scheduled to run on HPC clusters. In addition to the existing Oracle’s SGE scheduling capabilities, Geneious Server 1.1 now supports the Load Sharing Facility (LSF) from Platform Computing. The DeCypher Acceleration module for Geneious Server will also let researchers offl oad large sequence comparison jobs such as BLAST, HMMer or Smith-Waterman to TimeLogic DeCypher cards. Full genome assembly can be performed with data generated by Illumina, 454, SOLiD and Ion Torrent, with support for Pacifi c Biosciences’ SMRT data under development.
www.geneiousserver.com
SciFinder Mobile
Using smartphone technology, researchers can now access Chemical Abstracts Service’s SciFinder. With no need to download a special app, the new mobile platform is available to all SciFinder subscribers and allows researchers to use web- enabled smartphones to access Chemical Abstracts Service (CAS) databases. SciFinder Mobile is not restricted by IP address and provides unlimited access to SciFinder features, enabling users to look up a chemical substance, fi nd or confi rm a property for a substance, and review publications and references for an author or inventor. It is compatible with a wide range of smartphone operating systems, including Apple iOS, Google Android OS, Nokia Maemo and Symbian OS, and RIM BlackBerry OS.
www.cas.org
Grapher 9
Golden Software has released the latest version of its 2D and 3D professional graphing
program that enables users to convert their data into one of 54
customisable graph types. Grapher 9 features a number of upgrades, including support for Unicode fonts. This support allows international users to create and display text using characters from languages other than English, and to save and open fi les with Unicode characters in the path name.
SciTools
Integrated DNA Technologies (IDT) is providing free oligo design and analysis tools via its online SciTools suite. These software applications determine the properties of any oligo sequence entered, as well as mediating the intelligent design of assay conditions. The SciTools suite includes IDT’s customised OligoAnalyzer, PrimerQuest and RealTime PCR design tools, in addition to a dilution calculator, a resuspension calculator and an application for analysing oligonucleotide secondary structures. The OligoAnalyzer calculates the physical properties of any DNA or RNA sequence, including those
containing methylated, locked and phosphorylated bases. The tool provides important information for reaction optimisation such as oligo melting temperature range, GC content, length, molecular weight, optical density and extinction coeffi cient. In addition, users can utilise mFold to investigate the existence of reaction-inhibiting secondary structures. To avoid potential off-target effects and explore oligo specifi city, each sequence can be directly compared with all known nucleotide sequences using a link to the NCBI BLAST database.
www.idtdna.com/scitools
WEB EXCLUSIVE REVIEW
now online Unistat 6.0
www.scientific-computing.com/products
Users also now have the ability to move any label in a graph, including plot labels, axis labels, axis titles and graph titles – eliminating
overlapping text and keeping graphs readable and informative for highest impact. Users can also clip bar charts, fi t curves and confi dence intervals to any specifi ed limits. Grapher 9 operates in a Microsoft Windows environment with Windows XP SP2 or higher, Vista, 7, or higher.
www.goldensoftware.com
www.scientific-computing.com
JUNE/JULY 2011 5
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