BioMMED Service
All BioMMED service functions are provided to LSU-based investigators on a charge back basis. Typically, LSU researchers are charged only the costs of supplies, while most of the personnel costs are provided via support of participating LSU units.
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Agilent 2100 Expert B.02.06 - Agilent's 2100 expert software is based on the flexibility of the integrated 2100 expert platform. This powerful software is for the analysis of RNA, DNA, proteins, and cells. It is the only industry microfluidic platform capable of performing electrophoretic assays for RNA, DNA and proteins, as well as two-color flow cytometry. The Expert Software for the Agilent 2100 Bioanalyzer offers powerful data evaluation tools for all available assays, automatic and manual integration, smear analysis and many assay-specific tools. The Agilent Bioanalyzer has powerful data evaluation tools: single platform for all available assays, automatic and manual integration, smear analysis and many assay specific tools. Results tables and graphics allow easy instrument control and support standard and advanced user modes. Single click overlay as well as scaling and zooming features allow quick and easy comparison of up to 48 samples within one chip or across multiple chips. Multiple exportable data formats are available: xml, csv, html, pdf, wmf, jpg, tif and bmp for integration into presentations, for example, Laboratory Information Management Systems (LIMS). The Agilent has free data review software that enables offline evaluation and sharing. It has improved and integrated diagnostic and troubleshooting to minimize system downtime. The software employs unique RNA Integrity Number (RIN) algorithm for unbiased total RNA integrity assessment. The color coded Result Flagging Tool is an easy to use, rule defined system for automated result display. Native XML file format allows for seamless data integration across platforms and projects. |
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MacVector 10.5.3 - MacVector is a general DNA and Protein sequence analysis, manipulation and documentation program. It features an intuitive interface that integrates a wide variety of industry standard analysis and data mining algorithms into a single application. High quality Quartz PDF graphics let you prepare stunning figures for publication. Simple point and click sequence manipulation features let you quickly create new DNA molecules using the same approaches you would use in the lab. |
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SoftMax Pro 4.7 - SOFTmax PRO allows you to create files containing all of the parameters required for acquiring and analyzing data from any MDC Microplate System instrument (you may also import data from other Molecular Devices instruments for display and analysis). SOFTmax PRO allows you to set up and run a complete assay. Instrument settings can be saved as a protocol file and used repeatedly for reading different microplates. All stand-alone instrument functions can be controlled using the software. In addition, SOFTmax PRO provides capabilities that are not available when using MDC Microplate System instruments in stand-alone mode (for example, user-defined Kinetic run times, read intervals, Automix parameters, and more). SOFTmax PRO collects and stores all raw data received from the instrument. Data is displayed on the computer screen in a grid format that corresponds to the wells in a microplate (all instruments) or individual cuvettes (SPECTRAmax PLUS or PLUS 384 only). How the data is shown depends on other settings made using the software. In addition to displaying data collected from an MDC Microplate System instrument, you may import, display, and analyze data collected from either a FLIPR or Criterion instrument. You can reduce the data using built-in formulas or you can define custom reduction formulas. More than one reduction can be shown and results from different microplates and/or cuvettes can be compared within the same experiment. |
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Primer Express 3.0 – Primer Express 3.0 is a primer and probe design tool. It lets you design oligonucleotides for PCR applications using a customized application specific document for 1.) Absolute/Relative quantification and 2.) Allelic Discrimination. Besides the primers, Primer Express 3.0 helps in designing the labeled probes, selection of the appropriate reagents (ex. TaqMan, PCR Master Mix), use of universal thermal cycling parameters and use of default primer and probe concentrations (or optimizing if necessary).
Sequence Detection System 2.3- The Enterprise edition of Sequence Detection System (SDS) Software from Applied Biosystems is a high-throughput application for storage, organization and analysis of large amounts of gene expression and genotyping data on the 7900HT real-time PCR system. Version 2.3 of the Sequence Detection System Software includes flags and filters for increased quality control, problem notification, filtering and troubleshooting and much more. Whether you choose absolute or relative quantitation methods, the software completely automates data analysis, and can automatically set the optimal baseline for each well, as well as the optimal threshold for each primer and probe set (TaqMan® Assays) or assay-specific primer set (SYBR® Green Dye). To quantitate the amount of target in unknown samples, the 7900HT system measures the sample’s CT (PCR cycle at which a statistically significant increase in reporter fluorescence can be detected above the background) and uses a standard curve to determine starting copy number. To prepare the standard curve, the software first calculates CT values from dilutions of samples with known starting copy number. The software then plots the log of the starting copy number against the measured CT value. The relationship between CT and starting copy number is linear over at least five orders of magnitude. Relative quantitation is ideal for gene expression studies. Instead of using a standard curve, expression levels are calculated relative to a calibration sample—saving you time and money. An endogenous control is used to normalize the sample amount. This method, coupled with the ability of the 7900HT system to quantitate both the target and endogenous control in a multiplex reaction, enables highly cost-effective, high-throughput gene expression studies. The relative quantitation (RQ) study allows simultaneous analysis of up to ten plates of data. This novel software tool analyzes all RQ studies, provides a plate-centric view, table settings, and plate/study-level flags and filtering capability. The software displays filtered data as a plot and exports the file, making RQ Manager easy to use and a valuable resource for all gene expression applications. For easy, automated troubleshooting and quality control, RQ Manager also includes flags and filtering capability that can be configured for absolute/relative quantitation, allelic discrimination, and analysis failure. Flags are specific to the type of analysis—average quantiation (AQ), relative quantitation (RQ), or allelic discrimination (AD).
Sequence Scanner 1.0 – This software allows users to view, edit, print, and export sequence data from the company's genetic analyzers. It also displays "thumbnail" traces to provide an overview of large amounts of raw sequence data and help identify anomalies. It allows you to view simultaneously the analyzed and raw trace data for a single trace, and also spot sample failures readily with reports such as the Plate Report. Files can be exported from Sequence Scanner Software in a number of files formats including jpeg and pdf files, either individually or in batch mode.
7500 Fast System Software – This powerful, flexible software is used for 7500 fast system file analysis. It includes automated analysis tools such as RQ Study (Relative Quantitation) gene expression analysis software allow the simultaneous analysis and visualization of up to ten 96-well plates of data. This powerful and user-friendly software includes: auto-baseline and auto-threshold for simplified data analysis, absolute quantitation of nucleic acid targets with the ability to simultaneously analyze multiple standard curves on a single plate, improving your workflow and easing the burden of downstream analysis, RQ (Relative Quantitation) gene expression analysis software with powerful data viewing capabilities allowing the simultaneous analysis of up to ten 96-well plates of data, automated SNP genotype calling capability, including 2-cluster calling, with intuitive graphical output and quality-value assignment, makes SNP analysis simple and straightforward, simple dissociation curve data collection and viewing, tool tips for easy identification of sample wells when viewing amplification curve or SNP genotyping plots. |
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Sequencher is the biologists’ choice for DNA sequence assembly and analysis software. Sequencher version 4.8 includes: multiple, configurable DNA assembly algorithms, comprehensive DNA sequence editing tools, full support of sequence data confidence values, powerful Reference Sequence and the Variance Table find SNPs quickly and easily, comprehensive Restriction Mapping, extensive data import & export capabilities, including customizable GenBank Feature handling specialized tools for Forensic mtDNA profiling, and comprehensive HTML Help throughout. Sequencher is a Deoxyribonucleic acid (DNA) sequence assembly and analysis software designed to be easy to use, fast, and powerful enough to handle virtually any DNA sequencing need. Improvements include: improved sequence features, enhancements to the Variance Table, Better Translation Tools, and Contextual Menus. New to this version is a Translated Variance Table that allows filtering of the results in the Table, new printable reports, and a SuperPro Key support. |
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Image ProPlus 5.0 - Image-Pro Plus is the ultimate image analysis software package for fluorescence imaging, quality assurance, materials imaging, and various other scientific, medical, and industrial applications. The most powerful member of the Image-Pro software family, Image-Pro Plus includes extensive enhancement and measurement tools and allows you to write application-specific macros and plug-ins. Powerful 2D and 3D image processing, enhancement, and analysis software with extensive measurement and customization features. |
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Lasergene 7 Package |
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EditSeq - EditSeq is a sequence editor and import/export tool. A sequence saved using EditSeq in Lasergene DNA or protein sequence format may be opened by any other Lasergene module. EditSeq shows the DNA or protein sequence and associated comments and features in three adjustable panes; to enter a new sequence, type in the appropriate IUB nucleotide or protein codes. Once you have entered a sequence, you may elect to block residues into triplets, columns of ten, or another grouping of your choice. Check the accuracy of the sequence using EditSeq’s proofreading and voice verification features. EditSeq’s search functions let you find positions and open reading frames instantly. Furthermore, you may invert, complement, or view statistics about any sequence or portion of a sequence. You can also translate a DNA sequence or back-translate a protein sequence using customized, expression-specific genetic codes. |
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SeqMan - SeqMan provides all the tools you need to assemble from two to tens of thousands of reads into contigs. Prior to assembly, SeqMan can eliminate poor quality data, vector sequence and contaminating data from your projects. Most importantly, for projects that utilize data from automated sequencers, SeqMan includes DNASTAR’s unique Trace Quality Evaluation system. This system evaluates the quality of the underlying trace data, and then generates the most accurate consensus sequence possible. You may configure SeqMan to apply all these tools automatically, saving countless hours of analysis and editing. |
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GeneQuest - GeneQuest helps you locate genes, regulatory elements, patterns and structure in your primary DNA sequence. GeneQuest's comprehensive set of analytical methods can be easily applied and manipulated for projects of any size - small, BAC-sized or even larger. You can easily compare sequences with existing genome and EST data using the integrated BLAST feature*, and find out more about related sequences using the integrated Entrez search tool*. GeneQuest also provides annotation and visualization tools so you can document your discoveries for your own use or for publication or submission to public databases. GeneQuest is one of the elements of the DNAStaR Lasergene package that facilitates the identification of features in DNA sequences. |
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MegAlign - MegAlign offers you a choice of four pairwise and four multiple sequence alignment methods for aligning nucleic acid or polypeptide sequences. Enter your own sequences or load public data directly from NCBI*. If you want to find more related sequences for alignment, simply run a BLAST query or utilize the Entrez text query interface*, then drop in the sequences you want from the list of matches. Easily customize views of alignments to highlight the similarities or differences of the sequences. Differences in chemical, structural or functional characteristics between sequences can also be displayed as well as your own groupings or consensus. You may create a subalignment from the current alignment by simply selecting a sub-region. MegAlign also enables you to construct phylogenetic trees, generate detailed numerical reports or export data of sequence comparisons. Whether you want to compare gene families or sequence pairs, MegAlign provides you with flexible tools for customizing output for presentation and publication. MegAlign generates pairwise and multiple sequence alignments of DNA or protein or a combination of the two quickly and accurately. MegAlign can also create phylogenetic trees, as well as reports and tables showing the numerical data underlying the comparisons. |
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PrimerSelect - PrimerSelect's comprehensive set of tools enables you to design and analyze primers for PCR, sequencing, probe hybridization and transcription. Enter your own primers or let PrimerSelect generate a sorted list of suggested primers for all or part of your DNA, RNA or back-translated protein template. You can accept PrimerSelect's top choice, evaluated on the thermodynamic properties for annealing reactions, or view all of the options and choose alternatives based on your specialized knowledge. PrimerSelect includes the WorkBench where you preview the effects your choices will have on reading frames and restriction sites. PrimerSelect further assists you by highlighting potential pitfalls in both standard and multiplex PCR experiments via illustrations, graphs and statistical reports. These tools enable you to limit investment in time-consuming and costly experiments to those that have the highest probability of success. PrimerSelect even lets you perform BLAST or Entrez text searches and load sequences directly from NCBI's databases. |
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Protean - Protean helps you predict and display patterns, secondary structural characteristics and physicochemical properties of protein sequences via its comprehensive suite of protein analysis tools. Protean's simple, elegant graphical user interface can also help you locate antigenic determinants and predict protease digestion patterns. When you find interesting structures, you can utilize the integrated BLAST tool* to search NCBI's databases for related sequences using all or part of your polypeptide as the query. Protean also provides you with the tools to easily annotate and export your findings as reports, pictures or tables. |
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SeqBuilder - SeqBuilder enables you to edit nucleic acid and amino acid sequences and view the sequences and related items in multiple ways. SeqBuilder's window can be split into multiple panes so that more than one view can be displayed at any time. The possible views include a residue-specific view, a linear map, a circular map, a compact map of restriction cut sites (mini map), as well as a list of features, a summary of all restriction cut sites, and any comments. Each view lists a number of items that can be individually turned on or off including features, restriction sites, translations in all six reading frames, ORFs, and rulers. Many of these items can also be positioned and modified to emphasize certain characteristics. Dynamic links between the sequence and its annotations automatically update feature coordinates when you edit a sequence. Available functionality also includes the ability to reverse complement, translate, back-translate sequences, identify ORFs and perform BLAST and Entrez text* searches directly to NCBI or your personal DNASTAR StarBlast Server (sold separately). SeqBuilder's editing capabilities are also integrated into many other Lasergene modules. Edits made in SeqBuilder will be shared automatically with other Lasergene applications that are analyzing the same data, making SeqBuilder an integral member of the powerful Lasergene suite. |
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AlphaEaseFC (FluorChem HD2) – AlphaEaseFC software includes image optimization tools that adjust contrast automatically or manually. Converting the image from positive to negative, using digital filters, applying a false color map, or other such techniques can be used to clarify hard-to-see portions of the image. Notes, labels, arrows, lines, and other drawing tools can be recorded directly onto the image using the AlphaEaseFC software’s annotation functions. Annotations are superimposed on the image upon hard copy printing and can either be saved as a template file or as part of the image. All AlphaEaseFC features are accessible via convenient on-screen buttons and menus in an intuitive, mouse-controlled interface. AlphaEaseFC software also includes a broad array of analysis tools, including molecular weight calculation, Rf determination, 1-D lane densitometry, 2-D spot densitometry, quantitative PCR, microtiter plate reading, object distance measuring, gel scoring, and automatic colony counting. |
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SigmaPlot 10.0 - SigmaPlot graphing software from SYSTAT takes you beyond simple spreadsheets to help you show off your work clearly and precisely. With SigmaPlot, you can produce high-quality graphs without spending hours in front of a computer. SigmaPlot offers seamless Microsoft Office integration, so you can easily access data from Microsoft Excel spreadsheets and present your results in Microsoft PowerPoint® presentations. SigmaPlot 10.0 gives the exact technical graph type needed for demanding research. And, to help see interactions in 3-D data, SigmaPlot powerfully renders multiple intersecting 3-D meshes with hidden line removal. With so many different chart and graph types to choose from, users can always find the best visual representation of data. |
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GraphPad Prism 5.0 - GraphPad Prism helps you organize, analyze and graph repeated experiments, pick appropriate statistical tests and interpret the results. This makes it ideally suited to data plotting and analysis applications in the life sciences. What makes Prism truly unique, however, is not just what it does, but how it does it. Designed for laboratory and clinical researchers, Prism doesn't expect you to be a statistician. It guides you through the analysis process – giving you as much help as you need – and tracks and organizes your work like no other program available. You can concentrate on your data, not on figuring out how to use the program. Prism makes it very easy to perform basic statistical tests commonly used by laboratory researchers and clinicians. It does not take the place of the big statistics programs, however it offers a complete set of statistical analyses up to two-way ANOVA, including analysis of contingency tables and survival curves. Prism does not perform ANOVA higher than two-way, or multiple, logistic or proportional hazards regression. With Prism you can store all parts of an experiment (several data tables linked to results, graphs, page layouts and notes) in one organized file. You can decide how much information to include in one project file. You can place all your data tables into one file, along with linked results and graphs. Or you can also separate your work into lots of files. Prism lets you choose how to organize your work. |
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Adobe Photoshop CS3 – Photoshop is the professional standard in digital imaging, with an endless selection of drawing tools, filters, and color-adjustment capabilities for manipulating items in almost any way. Originally designed for bitmap images, Photoshop lets you create eye-catching typography by placing text on paths or within shapes, perform shadow and highlight correction, explore expanded color-matching features, parlay efficient layer comps, and preview, search, and share images. CS3 Extended includes support for rendering and integrating 3D images into 2D composites and video layer editing. There's also a greatly modified help menu to take the edge off your learning curve, with built-in how-to's on Preparing Art for Other Applications, Printing Photos, Working with Color and Type, and more. From simply lightening dark photos to improving color and contrast, to adding objects or people that weren't originally in the picture, Photoshop is an excellent tool whose innovative features meet any professional need. |
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Adobe Acrobat 8 Professional - Adobe Acrobat 8 Professional for Windows software enables business professionals to reliably create, combine, and control Adobe PDF documents for easy, more secure distribution, collaboration, and data collection. Protect sensitive information with passwords, permissions, and digital signatures. Enable users of Adobe Reader software (version 7.0 or 8) to participate in document reviews, fill and save forms, and digitally sign documents. Adobe Acrobat is a family of computer programs developed by Adobe Systems, designed to view, create, manipulate and manage files in Adobe's Portable Document Format (PDF). Adobe Reader is available as a no-charge download from Adobe's web site, and allows the viewing and printing of PDF files. Acrobat and Reader are widely used as a way to present information with a fixed layout similar to a paper publication. |
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WINSCP3 - WinSCP is an open source free SFTP client and FTP client for Windows. Its main function is safe copying of files between a local and a remote computer. WinSCP3 can be used to access your personal space on our servers from any place that has an internet connection. Features: graphical user interface, translated into several languages, integration with Windows (drag&drop, URL, shortcut icons), U3 support, all common operations with files, support for SFTP and SCP protocols over SSH-1 and SSH-2 and plain old FTP protocol, batch file scripting and command-line interface, directory synchronization in several semi or fully automatic ways, integrated text editor, support for SSH password, keyboard-interactive, public key and Kerberos (GSS) authentication, integrates with Pageant (PuTTY authentication agent) for full support of public key authentication with SSH, explorer and Commander interfaces, optionally stores session information, optionally supports portable operation using a configuration file in place of registry entries, suitable for operation from removable media. |
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Microsoft Office 2007 Enterprise Edition |
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Excel 2007 - Microsoft Office Excel 2007 is a powerful tool you can use to create and format spreadsheets, and analyze and share information to make more informed decisions. Office Excel 2007 includes quick table formatting and a completely redesigned charting engine that will help you better communicate your analysis in stunning charts. Office Excel 2007 takes advantage of the Office Fluent user interface to make powerful productivity tools easily accessible. It also offers more room for you to work in and delivers faster performance. New data analysis and visualization tools help you analyze information, spot trends, and access your company information more easily. Office Excel 2007 makes sharing spreadsheets and business information easier. Integration with Excel Services and the new Microsoft Office Excel XML Format can provide a more efficient exchange of information. |
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Word 2007 - Office Word 2007 is a powerful authoring program that gives you the ability to create and share documents by combining a comprehensive set of writing tools with the easy-to-use Microsoft Office Fluent user interface. Office Word 2007 helps information workers create professional-looking content more quickly than ever before. With a host of new tools, you can quickly construct documents from predefined parts and styles, as well as compose and publish blogs directly from within Word. Advanced integration with Microsoft Office SharePoint Server 2007 and new XML-based file formats make Office Word 2007 the ideal choice for building integrated document management solutions. |
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Access 2007 - With its Microsoft Office Fluent user interface and interactive design capabilities that do not require deep database knowledge, Microsoft Office Access 2007 helps you track and report information with ease. Get started quickly with prebuilt applications that you can modify or adapt to changing business needs. Collect information through forms in e-mail or import data from external applications. Create and edit detailed reports that display sorted, filtered, and grouped information in a way that helps you make sense of the data for informed decision-making. Share information by moving your Office Access 2007 files to a Windows SharePoint Services Web site, where you can audit revision history, recover deleted information, set data access permissions, and back up your information at regular intervals. |
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PowerPoint 2007 - Microsoft Office PowerPoint 2007 enables users to quickly create high-impact, dynamic presentations, while integrating workflow and ways to easily share information. From the Microsoft Office Fluent user interface to the new graphics and formatting capabilities, Office PowerPoint 2007 puts the control in your hands to create great-looking presentations. |
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Publisher 2007 - Microsoft Office Publisher 2007 helps you create, personalize, and share a wide range of publications and marketing materials in-house. New and improved capabilities guide you through the process of creating and distributing in print, Web, and e-mail so you can build your brand, manage customer lists, and track your marketing campaigns — all in-house. |
Last Updated Monday, May 04 2009 @ 10:16 AM CDT|28,331 Hits 
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