Life Science Software

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Biobar – Browsing toolbar for the Life Sciences

The biobar project is a bioinformatics power-browsing toolbar for Mozilla-based browsers. This toolbar provides access to major biological data resources. The primary advantage of this tool is that it allows a biologist to browse and retrieve data from Genomic, Proteomic, Functional, Literature, Taxonomic, Structural, Plant and Animal-specific databases. In addition to the browsing features, biobar also provides links to important bioinformatics sites and services including services at the European Bioinformatics Institute (EBI), National Center for Biotechnology Information (NCBI) and DNA Data Bank of Japan (DDBJ). The tool also provides links to major data deposition sites for nucleotide, protein and 3D-structure data. Finally, the menu also contains links to many Sequence, Structure alignment and analysis tools.

With version 1.3 of biobar it is possible to customize the search menu of the toolbar. The procedure involves editing an XML file and saving the file in your profile directory.

Browser: Firefox/Flock/Mozilla/Netscape and Seamonkey

Licence: Freeware

Software link:Biobar – Browsing toolbar for the Life Sciences

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ReaxFF is a new program for modeling chemical reactions with force fields based upon the reactive force field method of van Duin and coworkers. See: A.C.T. van Duin, S. Dasgupta, F. Lorant, F and W.A. Goddard III J. Phys. Chem. A 105, 9396 (2001). SCM has significantly optimized the original code in our implementation of this method. Memory bottlenecks have been removed, and the code has been parallelized. Systems consisting of a 3D box of multiple molecules totaling tens of thousands of atoms can now be modeled.

It includes parameters for many elements not included in traditional force fields, such as a number of transition metals. ReaxFF has been used over the past decade in various studies of inhomogeneous reactive systems, including solvent environments, interfaces, and molecules on metal and metal oxide surfaces.

A summary of ReaxFF's features:

molecular dynamics and minimizations using reactive force fields
model reactants, intermediates and products for systems of up to tens of thousands of atoms in a 3D box
Packmol builder for setup of complex systems of differing molecules
define different temperature regimes, pressure constraints, bond constraints, et cetera
analyze changing molecular composition during a reactive dynamics run

Software Link: ReaxFF - Program for Modeling chemical reactions

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Software for Continuous Flow and Flame AA Analyzers

NAP is a Windows®-based software and hardware package that collects and analyzes data from Continuous Flow Analyzers (including Technicon AAII, Alpkem RFA and Flame AA Analyzers) or any analog output capable instrument in +/- 0 to 5 volt range. Up to 6 instruments can be interfaced to one PC.
Complete data analysis including peak identification, run corrections and calculation of concentration values

Automatic QC and sample trend analysis plots
Direct interface to a LIMS or database
Optional software Control for pumps and sequential samplers
Available for Windows 2000®, Windows XP® Professional, Vista® Business

Data Collection and Calculations

Output from your instrument's detector is collected directly into NAP. A set of user-defined variables control peak analysis, allowing NAP to analyze a variety of peaks from different chemistries or instruments. Incoming data is displayed as it enters the system, peaks are identified, peak markers are displayed and concentration values are calculated automatically - all in real time! A time stamp is applied to each peak as it is identified, allowing you to report the exact date and time of analysis for each sample.

If samples are run on a regular basis, then default Sample Tables can be saved and loaded at run time. The NAP expansion function can automatically add repetitive samples and insert standards, QCs, etc., further reducing the time needed to set up a run.

Results are automatically corrected for Baseline Drift, Sensitivity Drift, Carryover, Dilution factors and Weight factors, using any number of correction samples. Spike recoveries are also calculated.

Standard calibration curves are created using a variety of linear and non-linear algorithms, including first, second and third order regressions and an optional function to force the curve through the origin. A single run can use multiple sets of standards. The system will be recalibrated as each new set of standards is run.

A Subtraction Channel automatically reports results for one channel subtracted from another. This can be used to report background corrected" values for specific analyses.

Run Automation

The new "Pause at End of Run" feature allows you to review a run

Software Link: NAP - Software for Continuous Flow and Flame AA Analyzers

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LabLite Stability Tracker is designed to improve communications and accountability between researchers and chamber (sample aging) areas. This program is an ideal fit for product testing and R&D facilities that need to manage and prepare sample lots for testing.

LabLite Stability Tracker was designed with the following goals in mind:

Speed communication between researchers and chamber areas
Manage and prioritize the research and chamber interchange
Track accountability and adherence to process
Provide reports and metrics needed for continuous process improvement

LabLite Stability Tracker met these challenges with a program that provides:

A simple yet powerful user interface
Built-in filters, and sort capability
Configurable setup and permissions

Communications - LabLite Stability Tracker provides a communication interface between researchers and chamber areas by allowing them to share comments regarding changes in lot, study, and chamber status. The program can include email notifications.

Manage Workload - LabLite Stability Tracker can minimize keystrokes and data entry errors by accepting study criteria directly from the researchers. Chamber personnel place the lots into chambers meeting lab-defined conditions, and can transfer all associated lot, study, and chamber information without repetitive data entry. LabLite Stability Tracker allows multiple reserachers the ability to see the status of their lots and studies anywhere in the process. User rights are definable.

Tracking - LabLite Stability Tracker provides a date/time stamp of every sample status change or action. This includes tracking when lots are moved between chambers or are pulled from chambers for testing. Items can be searched by date range, researcher, study, lot, product, unit, chamber etc... combining power, flexibility, and ease of use.

Reports and Metrics - LabLite Stability Tracker maintains study, lot, and chamber information throughout the aging process. Chamber and study specific reports can be produced electronically or in hard copy. Study details can be used to establish metrics or target areas for process improvement.

Software link: LabLite Stability Tracker - R&D management software

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Accelrys Biological Registration
Accelrys Biological Registration is the market's first multi-entity, fully-integrated system for registering, relationship-tracking, querying, and reporting on complex biological entities. Built in close collaboration with top pharmaceutical companies, this award-winning system helps you:

Protect your IP: Registering and relationship-tracking entities in a single, fully-integrated system ensures intellectual property (IP) protection, decreases safety and data integrity issues, and lets you record complete audit trails.
Improve operational efficiency: An integrated, easy-to-use, web-based system not only saves time by streamlining workflows, it also provides insights by letting you know what you're working with, who else is working with it, what others have done, how lineage may impact decisions, what batches have been manufactured , etc.
Meet current and future requirements: The ability to include your own entities, modify business-rules for registration, and expand the system makes this a solution that can easily adapt to your organization's changing needs.
Make better decisions, faster: Real-time reports and dashboards give managers the information they need, exactly when they need it.
Reduce total cost of ownership: The flexibility, scalability, and reduced complexity of the system means the total cost of ownership is lower than creating and maintain an in-house solution.

Software Link : Accelrys Biological Registration