Training and Support

FAQs

Tech specs

There are different system requirements for Pathway Studio depending on the installation platform. The minimum and recommended technical specifications can be found for each platform at the links below:

Pathway Studio web
http://help.elsevier.com/app/answers/detail/a_id/3179

Pathway Studio Desktop
http://help.elsevier.com/app/answers/detail/a_id/3180


 

For installation information about Pathway Studio Enterprise, please contact your sales representative, since these specifications are variable and dependent on the number of anticipated concurrent users.

FAQs

What is Pathway Studio?

Pathway Studio is an analytical solution for biological researchers and incorporates an expansive knowledge base of molecular facts that enable researchers to connect independent research findings to gain new insights, to analyze and interpret the results of biological experiments, and to build biological models to develop new hypotheses and to communicate and publish complex biological concepts.  Incorporating compelling interactive graphics, Pathway Studio helps researchers work more rapidly and with more confidence than performing manual research through articles.  It further helps avoid repeating previously conducted research, and can produce more compelling research conclusions from experimental process.

What data is included in Pathway Studio?

Pathway Studio comes in two basic data configurations that support human research or the research of plants.  These knowledge bases are protein-centric and support basic and applied life-science research.  The mammalian configuration can be additionally augmented with two data upgrades, ChemEffect®, a compound-centric knowledge base and DiseaseFx™, a disease-centric knowledge base.  These add-ons are of specific benefit to pharmaceutical research and have applications in biomarker discovery and drug repositioning.


Pathway Studio's knowledge base includes millions of facts (peer reviewed observations of interactions) relating biomolecules, disease, cellular processes, drugs, metabolites, and enzymes.  These facts include observations of binding, expression regulation, disease association, abstract relationships supported by observations, and specific quantitative observations under disease conditions.  These molecular facts are extracted by Elsevier's MedScan® text-mining software, from Elsevier's biological journals, articles received through a collaborative network of other leading third-party publishers, and also from MedLine abstracts.  In total, roughly 30 million articles and abstracts are processed to produce Pathway Studio knowledge bases.  These knowledge bases are updated regularly to capture the latest research findings.


The knowledge base also includes libraries of biological pathways that are expertly prepared by Elsevier scientists and cover topics of signaling, metabolism, cellular process, and disease.  Additional pathway libraries are provided that support robust experimental data analysis.  In addition to the pathway libraries, the knowledge base includes reference and ontological data taken from and linking to specific authoritative sites such as EntrezGene, PubChem, and GenBank.  The reference data establishes standards based identifiers that enables molecular observations to be integrated across independent studies.

Who can benefit from Pathway Studio?

Pathway Studio complements traditional biological workflows in life sciences and in industry, supporting fact gathering to summarize knowledge and to obtain new insights, experimental data analysis, and development and communication of new hypotheses.   Pathway Studio is broadly used by bench level scientists, bioinformaticians, and in-silico biologists that need to rapidly build upon established findings to address modern research challenges.

Does Pathway Studio require installations?  Does Pathway Studio come in a web-based configuration?

Pathway Studio comes in two configurations to span the needs of researchers.


Pathway Studio Web can be accessed from all modern browsers and taps into a constantly updated stream of facts derived from the latest research publications. Maintained and operated by Elsevier from a centralized server, the system is always available and provides high-performance.


Pathway Studio Enterprise is our premier offering providing unlocked flexibility and power to organizations addressing the most pressing research challenges. Pathway Studio Enterprise is avuaibale as a cloud application or as installed software on your infrastructure. Pathway Studio Enterprise also comes with powerful application programming interfaces (API) that let you integrate Pathway Studio into your own research infrastructure and Elsevier proprietary text-mining technology, allowing companies to better leverage their legacy data and information.

May I have a demonstration of Pathway Studio free of charge?

Yes, please contact sales to register a demonstration.

Is a username or password needed to access Pathway Studio Web?

Pathway Studio is offered on an annual subscription basis on a named-user basis, providing you with a username and password that will work anywhere.  Alternatively, we offer CWA-licenses (Corporate/Campus Wide Access) flat-rate on a yearly subscription basis including user authentication via IP-recognition - so no credentials needed here – no seat-based delays or budgetary concerns about task-based searches.

Is it possible to link to full-texts of journals and publications?

Yes.  Over 15 million sentences are integrated to support the facts contained in Pathway Studio knowledge base so that users can reference the underlying context of the facts and ensure a fit with their specific research.  References facilitate a researcher to link out to the underlying article.

What kind of experimental data can Pathway Studio accommodate?

The primary types of experimental data supported in analysis by Pathway Studio include:

  • Gene expression,
  • Proteomics, and
  • Metabolomics.
  • RNA-Seq.

Additionally supported include

  • Methylation,
  • Phosphorylation,
  • Genome Wide Association Studies, and
  • virtually any experimental data that can be expressed in a tab-delimited file consisting of an identifier for gene, protein, small molecule, disease, etc. along with a numeric value.

Pathway Studio Enterprise enables the simultaneous analysis of multiple data types.

What are typical questions researchers may answer using Pathway Studio?

  • What is known about disease x?  What proteins are involved with the disease?  How are genes regulated in this disease?
  • For my gene/protein of interest, what genes / proteins regulate its expression?  What does it regulate downstream?
  • For my list of genes / proteins, how do they interact?  What cellular processes are most involved with them?  What compounds bind my protein.
  • In my gene expression experiment, what are the key regulators?  What biological pathways are most implicated as being regulated in my experiment?  What cellular processes are most implicated as being regulated in my experiment?  What miRNA are statistically implicated to regulate my gene expression results.
  • What proteins are downstream of my target protein that have evidence of being assays which might be potential biomarkers.
  • Can I develop a graphic model of disease mechanism for publication?

How does Pathway Studio deal with firewall security?

Security is one of our biggest concerns and therefore Pathway Studio Web is accessible using HTTPS protocol.  This requires port 443 to be open in a company's firewall.  Since this is a standard setting, users should have clear access to Pathway Studio Web from within their company environment.


Pathway Studio Enterprise is natively installed behind your company's firewall, which eliminated access issues.

Can customers link in-house data with Pathway Studio?

Yes, Pathway Studio Enterprise has robust support for this activity


Please contact sales for more information.

Do CWA and web-based access also allow for individual saved searches?

Yes.  Both Pathway Studio Web and Pathway Studio Enterprise support login accounts for saving imported experiments, analytical results, and pathways.


For Pathway Studio Enterprise, your company's application administrator can create user accounts for access.  Alternatively, Pathway Studio Enterprise can be integrated with your company's authentication system such as LDAP or ActiveDirectory.


With Pathway Studio Web, users with CWA access (IP authentication) can use the system in anonymous mode without saving results, or self-register for a login account so that results can be saved.

How do I access training and support for Pathway Studio?

In order to provide a superior user experience, Elsevier provides robust multichannel support. From within each product, customers have 24/7 access to on-line self-service support and training materials, including training guides, work flow examples and an FAQ knowledgebase, to provide guidance through the entire user experience. In addition, our Customer Care team stands ready to assist you through phone or email with any additional or unique questions you may have. Helping you to have a very positive and productive experience with Elsevier's products is our highest priority.

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