Life Science Software

CLC Assembly Cell - Genomics Software

CLC Assembly Cell is a high-performance computing solution for read mapping and de novo assembling of Next Generation Sequencing data.

Details
CLC Assembly Cell is a high-performance computing solution for read mapping and de novo assembling of Next Generation Sequencing data.

The command-line interface of CLC Assembly Cell enables the functionalities to be easily included in scripts and other Next Generation Sequencing work-flows.

CLC Assembly Cell is utilizing SIMD instructions to parallelize and accelerate the assembly algorithms, making the program the fastest Next Generation Sequencing assembler at present.

The main functionalities of CLC Assembly Cell are:

Read mapping
Read mapping of Illumina Genome Analyzer, SOLiD, and 454 sequencing data
Support for native Color Space assembly
Support for both short read and long read assembly, including 454/Titanium data
Support for both gapped and ungapped alignments when doing short read assemblies
Support for assembly of paired end reads

De novo assembly
De novo assembly of Illumina Genome Analyzer and 454 sequencing data
Support for both short read and long read assembly, including 454/Titanium
Support for de novo assembly of paired end data

Other analyses
Fast analysis of raw data, including reporting
Option of joining data from different sources into the same analysis (including data generated by different kinds of sequencing technologies)
Extraction of data from part(s) of an assembly. Examples are extraction of contig and reads from an area of interest, or extraction (exclusion) of data from a specific sequencing lane that is suspected not to be of acceptable quality.
Find variations (simple SNP detection)
Support for input file formats Fasta, Sff, GenBank, csfasta, and scarf
A number of output options, including tables with assembly info
A "graphical" (ASCII art :-)) assembly viewer to get quick overview
Full integration with CLC Genomics Workbench. Output data from CLC Assembly Cell can be imported and further analyzed in CLC Genomics Workbench.

Software Link: CLC Assembly Cell

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CLC Genomics Machine is a turnkey solution including a lightning fast hardware platform with pre-installed enterprise software focusing on High-Throughput Sequencing data analysis - ready to function straight out of the box.
Details
Turnkey solution for large full-genome analyses

CLC Genomics Machine is a turnkey solution including a lightning fast hardware platform with pre-installed enterprise software focusing on High-Throughput Sequencing data analysis - ready to function straight out of the box. In addition, CLC Genomics Machine comes with several CLC Genomics Workbenches for user-friendly NGS data analysis on your own desktop.

Features
CLC Genomics Machine is a turnkey solution providing your organization with a wide range of High-Throughput Sequencing data analysis tools. Some are shown below:

Genomics
Read mapping of Sanger, 454, Illumina Genome Analyzer and SOLiD sequencing data
De novo assembly of genomes of any size (only limited by RAM available)
Color space mapping
Advanced visualization, scrolling, and zooming tools
SNP detection using advanced quality filtering
Support for multiplexing with DNA barcoding

Transcriptomics
RNA-seq including support for paired data and transcript-level expression
Small RNA analysis
Expression profiling by tags
EST library construction
Advanced visualization, scrolling, and zooming tools
Gene expression analysis

Epigenomics
Chromatin immunoprecipitation sequencing (ChIP-seq) analysis
Peak finding and peak refinement
Graph and table of background distribution and false discovery rate
Peak table and annotations

Software Link: CLC Genomics Machine

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CLC Genomics Server is an advanced High-Throughput Sequencing focused three-tier solution offering secure, powerful, and flexible bioinformatics computing on a server-architecture located centrally in your organization.
Details
Centralized Bioinformatics Analyses

CLC Genomics Server is an advanced High-Throughput Sequencing focused three-tier solution offering secure, powerful, and flexible bioinformatics computing on a server-architecture located centrally in your organization.

Available bioinformatics analyses
Read mapping of Sanger and High-Throughput Sequencing data
De novo assembly of Sanger and High-Throughput Sequencing data
SNP detection on whole genomes of any size
DIP detection on whole genomes of any size
ChIP-seq analysis
RNA-seq analysis
Small RNA analysis
Trim Sequences

Main reasons to invest in CLC Genomics Server
Compute Resource Management:
Central execution platform with flexible queuing system, designed for your bioinformatics analysis and services.
Flexible:
Based on a 3 tier system architecture to offer maximum security and intractability within fields of biology and bioinformatic computing.
Premium System-Clients:
Offers maximum client-flexibility with support for our user-friendly and award winning CLC Genomics Workbench as a premium system-client.
Customizable:
Highly customizable on both client-side and server-side using our SDK or various Command Line Tools.
Scalable:
Highly scalable with support for CLC Server Nodes.
Advanced Data I/O:
Offers an advanced and customizable data-import/export framework, that also can be used for data conversion.
Shared Data:
Store your data on central storage. This can be either a File System, the CLC Bioinformatics Database or on a custom designed database scheme.

Design custom workflows to support your science
With the Command Line Tools of the CLC Genomics Server, it is possible to define your own workflows. This is done in terms of scripts that interact with the CLC Command Line Tools. With the solution a sample script workflow is given, that imports NGS reads, maps the reads to a reference, followed by SNP and DIP detection:

Software Link: CLC Genomics Server

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We have overcome the challenge to analyze High-Throughput Sequencing data faster than it is produced by implementing a SIMD-accelerated assembly algorithm in our Next Generation Sequencing solution, CLC Genomics Workbench - a cross-platform desktop application with a graphical user-interface.
Details
Dominating the High-Throughput Sequencing data analysis challenge

We have overcome the challenge to analyze High-Throughput Sequencing data faster than it is produced by implementing a SIMD-accelerated assembly algorithm in our Next Generation Sequencing solution, CLC Genomics Workbench - a cross-platform desktop application with a graphical user-interface.
CLC Genomics Workbench, for analyzing and visualizing Next Generation Sequencing data, incorporates cutting-edge technology and algorithms, while also supporting and integrating with the rest of your typical NGS workflow.

Some of the key Next Gen Sequencing applications of CLC Genomics Workbench are listed below

Genomics
Read mapping of Sanger, 454, Illumina Genome Analyzer and SOLiD sequencing data
De novo assembly of genomes of any size (only limited by RAM available)
Color space mapping
Advanced visualization, scrolling, and zooming tools
SNP detection using advanced quality filtering
Support for multiplexing with DNA barcoding

Transcriptomics
RNA-seq including support for paired data and transcript-level expression
Small RNA analysis
Expression profiling by tags
EST library construction
Advanced visualization, scrolling, and zooming tools
Gene expression analysis

Epigenomics
Chromatin immunoprecipitation sequencing (ChIP-seq) analysis
Peak finding and peak refinement
Graph and table of background distribution and false discovery rate
Peak table and annotations

Cross-platform
CLC Genomics Workbench is available for Windows, Mac OS X, and Linux platforms, and includes all features of CLC Main Workbench for carrying out a wide range of downstream analyses.

Benchmarking
In benchmark tests we have assembled half a million 454 reads against the full E. coli reference genome in around 2 minutes on a two-core laptop with 2 gigabyte RAM. This speed-up, based on integrated SIMD high-performance computing technology, increases even more when using a computer with more CPU-cores and RAM.

454, SOLiD, Illumina Genome Analyzer - no problem!
We support all the major Next Generation Sequencing platforms, such as SOLiD, 454, Illumina Genome Analyzer and of course also Sanger. We are working closely together with all the instrument vendors to ensure full integration in the ongoing development.

Software Link: CLC Genomics Workbench

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Mascot Cluster is a complete, turn-key solution for high throughput protein identification.

Mascot has been designed to be embarrassingly parallel, which means that each search can be divided to run in parallel on multiple processors. Support for parallel execution is built-in to Mascot, and does not require any special operating system or grid engine. If you wish, you can license the software and set up a cluster using your own hardware. On this page, we describe the other option: a turn-key system with Mascot pre-installed on reliable, high performance IBM hardware.

Hardware

Any current IBM server that uses Intel or AMD processors can be used as the hardware platform. For a small cluster, up to around 6 processors, the most cost-effective solution is to use a number of dual processor servers, either tower or rack mount. For larger systems, we recommend the IBM BladeCenterTM, which is more compact and easier to manage than a large number of standard servers.

Mascot licensing is socket based. That is, if a processor has multiple cores, Mascot will use all of them for searching. For a given architecture, search speed (or throughput) goes as the processor clock speed multipled by the total number of cores.

Only the processors used for searching require a Mascot licence. It is often a good idea not to run searches on the master (head) node of the cluster, but leave it free to run the web server, handle database updates, and generate reports. This makes the server very responsive even when there are several searches running, using all the processor time on the search nodes. Having a non-searching master node also gives you a spare node, in case one of the search nodes has a hardware failure.

Result files are stored on the master node, so this needs access to plenty of disk storage. Search nodes only need local storage for program files and the compressed sequence database files; a single hard drive of modest size is usually sufficient. All nodes should have at least 2 GB RAM.

Software Link: Mascot Cluster - Spectroscopy Software

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PharmaExpert analyzes the relationships between biological activities, the interactions of drugs and the multiple targeting actions of chemical compounds. As a pharmacological knowledge-based tool, it provides in silico screening of compounds using PASS prediction results.

Details
Key features of PharmaExpert:
• Mechanism-effect relationship (MER) base, manually curated by experts, contains 11,049 mechanism-effect relationships
• Selection of compounds with required therapeutic but without side effects
• Comparative analysis of compounds with similar structures
• Selection of compounds with multiple mechanisms of action
• Analysis of drug-drug interactions with regard to their pharmacokinetic, pharmacodynamic and adverse effects

PharmaExpert is an addition to the PASS (Prediction of Activity Spectra for Substances) tool. It provides a comfortable solution for data mining of the PASS prediction results to find the best drug-like candidates from a set of compounds. The core of the program is a mechanism-effect relationship (MER) base, manually curated by experts, which is used to determine cause-effect relationships for the compounds. Like PASS, the software runs under Windows.

PharmaExpert has been developed by Vladimir Poroikov, Dmitry Filimonov & Associates currently working in the Department for Bioinformatics at the Institute of Biomedical Chemistry, Russian Academy of Medical Sciences in Moscow.

A free demo version, as well as further information, is available upon request.

Software Link: PharmaExpert - Pharmacology Software

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Mascot Daemon is a client application which automates the submission of data files to Mascot server. It runs under Microsoft Windows 2000, XP, Server 2003, Vista, Server 2008, and 7. Daemon functionality includes:

Batch mode, in which an arbitrary group of files can be defined for searching, either immediately or at some pre-set time.
Real-time monitor mode, in which new files on a pre-defined path are searched as they are created.
Score dependent follow-up tasks. For example, automatically repeating a search at a later date or against a different sequence database.

Multiple Daemon clients can submit searches to a single Mascot server. If you have several mass spectrometers, you can install separate copies of Daemon on each instrument data system or just have a single copy of Daemon somewhere on the LAN marshalling searches for all instruments.

The functional unit of Mascot Daemon is a task, which is defined by the data source (a list of data files or a file path), how the data are to be searched, when the searches are to take place, and any follow-up activities, such as conditional repeat searches.

Search parameters are defined in the Parameter Editor, which closely resembles the HTML form used for interactive Mascot searches. Fields can also contain HTML-like tags which are automatically substituted at run time with information such as a file name or a sample description.

Every time a new task is run, it creates a task node on the status tree. The results from each task are attached to the task node, just like directories and sub-directories in Windows Explorer. Key information for each result can be displayed by clicking on the result node. The full result report can be displayed in a web browser by clicking on the blue hyperlink.

Daemon's follow-up function is extremely powerful and can be used in many different ways. A couple of simple examples would be:

A batch of data files can be searched at specified intervals against database updates. Each data file will stay in the loop until it's score exceeds a pre-set level.
Sequence databases of increasing size or decreasing quality can be searched serially. For example, a small database of common contaminants such as keratins might be searched first. Spectra which are unmatched can then be searched against a comprehensive non-redundant protein database, such as NCBI nr. Data which still fail to find a match can then proceed to a search of dbEST.

Arbitrary numbers of follow-up tasks can be chained together to implement complex decision trees. This is only possible because Mascot scores reflect true probabilities, permitting rule based software to determine whether a match is significant according to user specified criteria.

The default database engine used by Mascot Daemon is Microsoft Jet 4.0, the engine used by Access 2000. Alternatively, Daemon can be configured to use any database engine which supports either OLE DB or ODBC, such as Microsoft SQL-Server or Oracle, enabling multiple Daemon clients to share a common task database.

Software Link: Mascot Daemon - Spectroscopy Software