Online Resources for Experimental Design
The information here is provided as a service to the scientific community about several online resources that can assist with your daily work and that are freely available.
Life science and systems biology research requires the integration of a number of information resources. Recognizing this challenge, scientists have come together to develop a growing number of websites and communities that aim to solve this puzzle. This online guide at www.invitrogen.com/linnea can assist lab managers with their own research needs as well as needs within their laboratories.
Specific areas of Focus Include:
- Gene & Protein Resources: LINNEA™ Genes is a powerful search engine that allows lab managers to quickly search through over 245,000 gene and protein based products from both human, mouse, and rat. This information resource also provides direct access to over 200 validated signal transduction pathways and contains scientific gene and protein information. The information in LINNEA™ Genes is sequence standardized and uses internationally recognized gene IDs and symbols within the reference ontology.
- Vector Sequence Software: Vector NTI® Software is freely available to lab managers through an open access policy for academic researchers. This application allows them to design, annotate, and store vector and primer sequences in the laboratory and effectively manage vector inventory.
- Protocol Resources: LINNEA™ Protocols provides over a 1,000 validated protocols from both Invitrogen and Current Protocols™ from John Wiley and Sons to assist them in lab training and experimental design.
Simplifying the task of gathering product and reagent information, LINNEA™ Genes provides a very powerful search engine that allows researchers to rapidly search through over 245,000 gene and protein products from human, mouse, and rat to find the right reagent. Search results can be filtered by a number of features including product category, application, and species. Supporting drug discovery, product lists organized by gene symbol and direct links to products by gene family within many of the common druggable gene classes are also provided. Behind these functionalities is a custom-designed relational database that holds standardized product information and gene and protein information relationships.
Understanding the complex dynamics and relationships within cell signaling is core to biological discovery. The search engine provides access to 248 signaling and metabolic pathway maps [maps provided by GeneGo (www.genego.com)]. Each map allows direct access to associated products and reagents to allow rapid investigation of pathways for important cellular processes.
Having desktop software and online resource to reliably facilitate reagent design and information management of DNA primers, RNAi molecules, and DNA vectors is key as data integration within the lab inherently saves time, allowing more time for research. Software solutions containing informatics analysis packages also allow researchers to gain new experimental insights and improve experimental designs prior to testing them at the bench.
Vector NTI® software is a powerful desktop tool for DNA and protein sequence analysis that has become a standard resource for a number of scientists within the life science industry. It is available free of charge to scientists from non-profit institutions directly through the Vector NTI® User Community (www.invitrogen.com). Commercial researchers can also access this site to obtain free trial licenses to evaluate the software.
Providing solutions for molecular biology and genomics, this tool allows users to design, construct, and analyze a number of biomolecules within the lab. Each new sequence or vector can be easily designed and viewed in silico prior to testing in the lab and new reagents can be ordered online from Invitrogen directly through the software. Integrating bioinformatics algorithms with real experimental data in their design, these resources are optimized for each reagent to provide the best solution.
To ensure the design of more successful, accurate experiments, a freely available, centralized, online collection of the best research practices and methods across life science research have been created. LINNEA™ Protocols houses a targeted selection of over 900 proven methods from Current Protocols™ by John Wiley & Sons, as well as over 1,000 validated experimental protocols developed by Invitrogen scientists. The protocol library supports common research workflows and quickly connects scientists to detailed experimental methods, supporting documentation, and recommended products for each experiment. This will allow lab managers to more easily find new protocols and reagents when the laboratory is moving into new areas or when new experimental approaches are required.
As we look to the future, we foresee an even greater need for access to centralized scientific information and will be expanding the online guides in the coming years as science advances and new bioinformatics algorithms are developed. As many of these freely available resources support the integration and sharing of scientific information as well as streamlining reagent selection for the lab, they significantly simplify researchers’ day to day work and free up more time for biological discovery — the end goal.
Michaeline Bunting, Ph.D., is the Director of eBusiness Sciences at Invitrogen. She received a Ph.D. in Biochemistry from the University of Utah.