Training and Support

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.  All convenient and without hassle.

Pathway Studio Enterprise is our premier offering providing unlocked flexibility and power to organizations addressing the most pressing research challenges.  Pathway Studio Enterprise is installed on your infrastructure and includes MedScan technology, allowing you to extend the knowledge base content with facts derived from internal literature or from subscription content you may have permission to process.  Pathway Studio Enterprise also comes with powerful application programming interfaces (API) that let you integrate Pathway Studio into your own research infrastructure.

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

Yes – please use CONTACT on www.elsevier.com/pathway-studio to request 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.

How reliable is the data in Pathway Studio?

The MedScan text-mining technology which produces the knowledge base has been in continuous development for over 10 years, supported by a statistically based quality improvement program.  ResNet Curator, our statistically based error resolution technology, is applied to the finished database to ensure quality.  The accuracy of our knowledge bases is sufficient to support robust statistical analyses and we believe the error rate is on par with manually curated data.   In contrast to manually curated data, MedScan brings us the ability to rapidly process all the available content without introduction of reader bias or selection bias.  We feel that the knowledge bases incorporated in Pathway Studio provide researchers an unparalleled source of information to support deep research activities.

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.

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?

This is not currently supported with Pathway Studio Web, however there is robust support for this with Pathway Studio Enterprise.

Please contact us 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. 

PATHWAY STUDIO™ DESKTOP 9 SYSTEM REQUIREMENTS

OPERATING SYSTEM

Windows XP Professional with Service Pack 3 (or later)*
Windows Vista (Home Basic, Home Premium, Business, or Ultimate edition)*
Windows 7 (Home Basic, Home Premium, Ultimate, Professional or Enterprise edition)*
*32-bit or 64-bit Edition supported, 64-bit Edition recommended.

RAM

Windows XP - 2 GB Minimum (3 GB recommended)
Windows Vista or 7 - 2 GB Minimum (4 GB or more is recommended)

MEDIA DRIVES

DVD-ROM drive (must be able to read dual layer DVDs) for execution of Pathway Studio® installation media

HARD DISK SPACE USAGE

ResNet® 9 Mammalian database - 15 GB*
ResNet® 4 Plant database - 3 GB
Pathway Studio® application, including MedScan Reader - 1 GB
MS SQL Server 2008, Workgroup Edition – 1 GB
*up to an additional 25 GB is required if additional databases, such as ResNet® ChemEffect or DiseaseFx, are to be installed.

OTHER REQUIREMENTS

NTFS file system
Microsoft Internet Explorer 7, or later
Microsoft .NET 3.5 SP1 (or 3.5.1) is required, and provided on the Pathway Studio® installation media or downloaded from Microsoft during installation.
Microsoft Windows Installer 4.5 is required, and provided on the Pathway Studio® installation media or downloaded from Microsoft during installation.
Microsoft MS-SQL 2008 Workgroup Edition is required, and is provided on the Pathway Studio® installation media and automatically installed during Pathway Studio® installation. If the installation finds an ARIADNE instance of MS-SQL 2005 Standard Edition already installed, the ResNet® database will be installed into that, and installation of MS-SQL 2008 will not be initiated. Note: use of MS-SQL requires a license agreement with Microsoft which can be provided by Elsevier at a discount when licensing Pathway Studio®.

Americas Tel: US toll-free: +1 (888) 615 4500 Tel: Non toll-free: +1 (314) 523 4900 Email: usinfo@elsevier.com Email Brazil: brinfo@elsevier.com

Japan Tel: +81 (3) 5561 5035 Email: jpinfo@elsevier.com Website: japan.elsevier.com

Asia & Pacific Tel: +65 6349 0222 Email: sginfo@elsevier.com

Europe and all other regions Tel: +31 20 485 3767 Email: nlinfo@elsevier.com

Pathway Studio Enterprise customers may contact pharmabiotecheh@elsevier.com