Geneious

Microsatellite Plugin now available

2012-10-30T01:11:16Z

From now until the end of May anyone can download a FREE Trial of the beta version of the Geneious Microsatellite Plugin.

The plugin has a simple interface to guide users through a workflow from import to allele calls. Data is stored safely in Geneious and can be easily exported to Excel to continue analysis.

Automation to speed up your research

Call peaks, match ladders and bin automatically

View genotype results in allele table views

Export peak calls and genotypes in CSV format for further analysis

Manual control of your data

Click and drag to adjust trimmed regions

Add and remove peaks for total control

Manually add, remove and edit bins including click and drag to resize

Zoom in and customize single or multiple traces

Features

Import traces in .fsa format and store them in the Geneious database

View a single trace or multiple traces simultaneously in the

zoomable, customizable trace view

Peaks are automatically called and ladder is automatically matched

Adjust trimmed region with click and drag

Manually add and remove peaks

Bins can be automatically called

Manually add, remove and edit bins including click and drag to resize

View results in the Alleles Table view

Export your alleles in CSV format for further analysis

False 250bp peak on GeneScan 500 automatically detected and removed

Choose yellow or black for NED trace

Export peak calls in CSV format

Export bins in CSV format

Allele size graph

Ladder fit graph

Undo and redo any changes

Analysis Parameters and Operating Conditions are imported from .fsa and saved in Notes

The Sponge Barcoding Project benefits from Geneious Biocode LIMS

2011-12-06T21:27:58Z

Sponges are among the most plentiful organisms on Earth, but are surprisingly challenging to sequence. DNA Barcoding projects are usually ambitious in scale, but many sponges require two barcoding fragments in order to be identified reliably at the species level – effectively doubling the PCR and sequencing workload.

To help speed up their workflows, the team on the Sponge Barcoding Project have leveraged the Geneious Biocode LIMS originally developed for the Moorea Biocode Project, another ambitious project to barcode an entire tropical island ecosystem. Coordinated at the GeoBio-Center at Ludwig-Maximilians University of Munich, the Sponge Barcoding Project is the first worldwide barcoding project on a non-bilaterian taxon, and covers the complete taxonomic range of Porifera (sponges).

Sponges play an important role in aquatic ecosystems, filtering particles including bacteria out of the water and forming a fairly substantial portion of our coral reef biomass. As one of the simplest of the conspicuous animal phyla, they lie at the base of the animal tree of life and are important subjects for considering the evolution of all animals. They are the most potent toxin producers among marine organisms, making their secondary metabolites valuable for drug development. One of the key challenges with sponges is that they are extremely difficult to distinguish accurately – both morphologically and with molecular techniques such as DNA barcoding.

To tell closely related sponge species apart the standard CO1 barcoding fragment is often not sufficiently different, so the team will supplement the standard fragment with 440 bp of more variable downstream sequence. In addition, standard barcoding primers tend not to work reliably with sponges or amplify the numerous commensals and symbionts. Therefore the project team had to develop sponge-specific primers, and even these have not always proven reliable among this interesting taxonomic group.

Prof. Dr. Gert Wörheide and the GeoBio-Center team are using the Geneious Biocode LIMS to process the first batch of 17,000 samples, provided by the Queensland Museum in Australia, home to the Great Barrier Reef and other Indo-Pacific locations. 25 institutes worldwide contribute to the project including the Ocean Genome Legacy in the US, the University of Bergen, and the Zoological Museum Amsterdam, in The Netherlands. Gert’s lab has extracted and sequenced the first batch of samples, and is cherry-picking holotypes and well known taxa for barcoding and uploading to the Sponge Barcoding Database. This will build the backbone database for species identification as a resource for future barcoding projects.

The lab uses the Geneious Biocode LIMS’ MySQL Connector to connect the lab's own FIMS, a MySQL database, with the Geneious Biocode LIMS and then perform their documentation extraction, PCR, sequencing and quality control. Sequences and assemblies are then stored on the lab’s own Geneious database.

“Previously we had to fill out endless Excel-files,” says Gert Wörheide. “With the Geneious Biocode LIMS we fully expect, after a short learning curve to adapt to a new system, that we will cut the time required by more than half.”

“It’s great to be able to use a LIMS that has already been developed and tested in the field for work similar to what we are doing. The support from Biomatters has also been excellent.”

When complete, the DNA-taxonomy and database for sponges is expected to have immense benefits for biodiscovery, ecology, conservation and the management of marine resources.

Geneious Biocode LIMS to be made freely available to DNA barcoding community

2011-12-06T21:45:37Z

The Laboratory Information Management System (LIMS) developed for the Moorea Biocode Project is to be made publicly available as a free beta version. The Biocode Project is an ambitious undertaking to create the first comprehensive inventory of all species larger than a microbe in a complex tropical ecosystem (Moorea in French Polynesia). Funded through a $5.2 million grant to UC Berkeley from the Gordon and Betty Moore Foundation, and based out of the American and French research stations on Moorea, Biocode brings together the Smithsonian Institution, the CNRS of France, and other partners.

The Biocode LIMS and data analysis components of the project were developed by Biomatters in collaboration with the Biocode Project researchers as a plugin for Biomatters’ Geneious Pro sequence analysis software. The Geneious Biocode LIMS will give biologists around the world a best practice tool to use in their own research as well as to freely access the Moorea project’s final database. An accompanying “Biocode Genbank Submission” plugin will allow researchers to upload their own sequence data from inside Geneious Pro directly to Genbank, the world’s largest public DNA sequence database.

The unique database of Moorea’s coral reef and terrestrial biodiversity will be publicly shared as a resource for ecologists and evolutionary biologists around the world. The Biocode LIMS has tracked over 24,000 specimens from over 30 phyla of algae, fungi, plants and animals in the first two years of the project.

Christopher Meyer, from the Smithsonian Institution and Director of the Biocode Project, says “The Moorea Biocode Project was created with the intention of providing a model system for similar comprehensive genetic inventories. In addition to tracking down all the biodiversity in this tropical island ecosystem, one of the promised deliverables has been an informatics tool to allow easy access to that data and to aid other genetic barcoding initiatives."

“We see no sense in reinventing the wheel. We want to share our best practices from this ambitious project with anyone, from single researchers, to a principal investigator's lab, to large scale initiatives like our own.”

The Biocode LIMS system provides an informatics pipeline for batch processing of samples from DNA extraction through to sequencing, identifying and re-running failed reactions, and identifying systematic errors that can be strategically addressed. It integrates with Geneious Pro’s existing sequence assembly tools and various Field Information Management Systems (FIMS), including TAPIR standard access protocols.

Once the specimen reaches the end of the pipeline, the Biocode Genbank submission plugin automates the submission of completed contigs to make the DNA sequences publically available. The reaction data from the LIMS database is combined with the field metadata from the FIMS database as a quality control mechanism including the completely tracked history.

Neil Davies, Director of UC Berkeley’s Gump South Pacific Research Station and Principal Investigator of the Biocode Project says, “This is the first freely available, broadly applicable software tool to assist tracking materials through the DNA barcoding pipeline. No other freely available program allows the level of tracking and data quality assurance through a lab system. Importantly, it goes beyond DNA barcoding to accommodate multiple genetic markers for use in a broad range of biodiversity and ecogenomic studies."

“The plate workflow approach taken has greatly simplified the process of identifying reaction failures, and setting them up to be run again. It manages data that used to be spread across multiple individuals and notebooks so we can search it, report success, or look for patterns. It has significantly reduced the human error that has been problematic in large-scale sequencing projects such as this in the past.

Says Meyer, “Our collaboration with Geneious has been absolutely critical for tracking workflows and maintaining the data integrity of the Biocode Project. Instead of starting from scratch, we got a leg up by joining forces with Biomatters and integrating with their existing Geneious platform”

Biomatters CEO Candace Toner says, “We’ve been working with the Moorea Biocode Project for over two years now and have developed the software under demanding real world circumstances."

“Most sequencing projects focus on one or two species, while Biocode focuses on an entire ecosystem and involves researchers from multiple international institutions. This creates challenges to organise the vast amounts of information produced and manage the sheer volume of human handling involved. For reproducibility and transparency, the Biocode LIMS needs to store a full, publically available lab workflow for each specimen.”

A beta version of the free Geneious Biocode LIMS and Geneious Biocode Genbank plugins are available from http://software.mooreabiocode.org. Users of the free Geneious Basic software will be able to access and view the Biocode database upon completion of the project, but a commercial copy of Geneious Pro is required for data creation and analysis.

To connect with the Biocode Project user community and technical support team, please visit the discussion forums or email support@mooreabiocode.orgsuppojrt@mokoreab2iocodje.orgs.

Key Features of the Geneious Biocode LIMS

Connect to field databases (FIMS) in Excel or TAPIR format
Search and retrieve data into Geneious from FIMS
Workflow tracking in tubes, 48, 96 or 384-well plates
Bulk tracking for DNA extractions, PCR and DNA sequencing reactions
Mark reactions as passed/failed
Cherry-pick passed/failed reactions to create new plates
Bin sequences based on quality
Verify taxonomy
Upload to Genbank
For more information, please see the Biocode Wiki

Watch the Video

A 20 minute introductory video on how to use the major features of the Geneious Biocode LIMS can be found here.

Geneious Server 1.0 released

2011-12-06T21:48:31Z

Two leading US government agencies are the first customers to purchase Biomatters’ new software package, Geneious Server™ – the Centers for Disease Control and Prevention (CDC) in Atlanta and the Walter Reed Army Institute of Research in Maryland. Prior to launch, an additional 12 institutions have been beta testing the new server software, including the DeRisi Lab at University of California San Francisco, The Samuel Roberts Noble Foundation in Oklahoma, BP Biofuels and the University of Queensland in Australia.

Dr Huo-Shu Houng, a Research Microbiologist in the Walter Reed’s Department of Viral Disease, says, “The move to Next Generation Sequencing required an investment in the software and management workflows to better handle the huge amounts of data that come with it. We compared the assembly results we get from the Geneious Assembler with the Roche de novo and reference mapping and we are particularly pleased with the quality of the Geneious assemblies."

Details About Geneious Server

Launched today, Geneious Server is a powerful sequence analysis software package for high-intensity computing such as Next Generation Sequencing (NGS), Phylogenetics and Sequence Analysis. With Geneious Server, you can offload your resource-hungry jobs directly from Geneious Pro™ on your desktop to Geneious Server, dramatically and easily speeding up your research.

Geneious Pro is the interface that connects you to the power of Geneious Server. When you run a job using an algorithm from one of the Geneious Server modules you have installed, you can choose to run your job on your desktop or push it to Geneious Server for increased computational performance. When your job is finished, your results are securely sent back to Geneious Pro with a message telling you the run is complete. It’s that simple!

If you are the proud owner of a cluster environment, multiple users can use Geneious Server as the staging platform to easily schedule and run jobs directly from their desktop to your cluster. This lets your users leverage the computing power of the cluster environment from the Geneious Pro interface that they know and love. No confusing configs or command lines, just drop down menus.

Geneious Server offers three core modules featuring powerful, peer-reviewed and trusted algorithms:

NGS Module featuring Geneious Assembler™, Velvet, MAQ, Bowtie, BWA
Phylogenetics Module featuring Geneious Treebuilder™, MrBayes, PhyML
Sequence Analysis Module featuring ClustalW, MUSCLE, MAFFT, MAUVE

Full genome assembly can be performed with data generated by Illumina™, Roche 454, SOLiD™, Pacific Biosciences and Ion Torrent machines.

Request Geneious Server Information for Your Institute

To contact us about implementing Geneious Server at your institution, get in touch through the Sales Enquiry form on our website.

Mining Global Ocean Sampling (GOS) Expedition metagenome data

2012-10-30T01:05:44Z

The explosion of metagenomic projects has opened the door for delineating the vast number of protein sequences obtained from a large diverse population of organisms. The wealth of sequence data is now available for any scientist who wants to identify homologous proteins sequences related to disease-associated pathways.

Geneious Pro software was used to examine putative leukotriene pathway proteins identified from the Global Ocean Sampling expedition metagenome data ... more

The full report is available here.

Cutting edge recombination detection - DualBrothers plugin released

2011-12-06T22:34:17Z

In partnership with Dr Marc Suchard of UCLA, Biomatters has released a plugin for DualBrothers – a freely available program for detecting recombination in multiple alignments. DualBrothers employs the most accurate method available to researchers today: the dual Multiple Change-Point (MCP) model.

Our plugin makes running this advanced analysis as easy as building an alignment and it's free for all Geneious users, both Pro and Basic.

Instructions
To install, select "Plugins" from the "Tools" menu in Geneious then click the "Install" button next to DualBrothers.

Once it's installed, run DualBrothers by selecting any multiple alignment and clicking "Detect Recomb." in the toolbar. To do a quick preliminary analysis, turn down the "Chain Length" option after clicking on Detect Recomb.

Geneious calculates graphs of your completed analysis – just click on the "Alignment View" tab.

More information

DualBrothers website: http://www.biomath.ucla.edu/msuchard/DualBrothers
Questions? Email feedback@geneious.comfeedbjack@gkeneio2us.cojms

Geneious Pro – Evolving Science Globally wins International Award for e-Science

2011-12-06T22:49:47Z

The Grand Jury of the World Summit Awards has declared Geneious Pro as a winner in the category of e-Science, and Best Practice of high quality e-Content for 2007!

The World Summit Award was launched as part of the United Nations Summit on the Information Society. It is a unique global competition for recognition of the ‘best of the best’ in e-Content and Creativity.

In September, the Grand Jury of the WSA met on the island of Brijuni bringing together eminent multimedia and e-Content experts from 32 countries to evaluate more than 650 entries nominated from 160 countries. Geneious Pro was selected by New Zealand as the best example of an e-Science entry, and was ultimately rewarded with the win!

Management from Biomatters will be attending the WSA 2007 Gala event in Venice, Italy on the 5th of November, followed by the Global Forum on IT on the 6th and 7th.