Plexus Suite FAQ

    What is Plexus Suite? Plexus Suite is a web-based collaborative data management and analysis system for chemical and biological research. Plexus Suite tools Plexus Suite has a modular structure. So far, two modules are available in an initial phase: Plexus Connect and Plexus Design.

    • Tools already released:

      • Plexus Connect: the major discovery user interface of Plexus Suite to access, display and query scientific data supporting grid- and form-based views. It provides multi-user web access to data. The data views can be created by the Instant JChem (IJC) form designer. Via Plexus Connects, IJC-generated grid and form views can be opened in a browser with most of the IJC widgets being supported. In Connect, you can browse, sort and search chemical structures and alphanumeric data; build and save queries and search hits as lists.

      • Plexus Design: the virtual library design solution of Plexus Suite. Synthetically feasible virtual compound libraries can be created in a few steps via scaffold based and reaction based enumeration. Plexus Design features a number of physicochemical properties characterizing molecules to help uderstand the libraries you create.

      • Plexus Mining: a unique data mining solution supporting chemically intelligent search. It features ChemAxon's mature naming technology, which supports the extraction of chemical information, such as names in various formats, embedded structures etc. fom any kind of documents.

    • What are the upcoming tools?

      • Plexus Analysis: a generic, web-based, integrable data visualization and analysis tool for scientists and industrial data analysts with strong chemistry, biology and statistical functions.

      • Plexus Registration: a tool for registering chemical and biological entities as concepts into a database as unique items. Getting Plexus Suite

    • Where can I try Plexus Suite?

      Please, contact us by email for a live demo of Plexus Suite.

    • How can I download Plexus Suite modules?

      Please, check the Plexus Suite product page for information on downloading modules or contact us by email. Licensing

    • Which licenses do I need to run Plexus Suite?

      In order to log in to Plexus, you will need a Plexus Conenct license. If you want to use additional features of the whole Suite (such as library design, data analysis...), you can use one or more from the other Plexus licenses (i.e., Plexus Design, Plexus Analysis, Plexus Registration).

      Plexus Suite uses the Marvin JS chemical editor, which requires the Marvin JS license. This license is automatically added to the generated license file, which we will send to you.

      If you intend to usse Plexus Suite with a remote database (e.g., Oracle or MySQL), you will need an Instant JChem Enterprise license as well.

    • Do I need an Instant JChem license, too?

      If you want to use Plexus Suite with a remote database, you will need an Instant JChem Enterprise license as well beside at least one of the Plexus licenses. Furthermore, since Instant JChem serves as an administrative interface of Plexus, the system administrator need it for managing user accounts, database views etc. System requirements

    • Which database engines are supported? Oracle, MySQL, MS SQL Server, or you can use local Derby databases as well.

    • Which web application servers are supported? You can deploy Plexus Connect through Apache Tomcat, or run it standalone by using the embedded Jetty.

    • Which web browsers can I use Plexus Connect with?

      Google Chrome, Mozilla Firefox, Internet Explorer 10+, Safari 7+. Hosted solutions

    • What are the options for using Plexus Suite as a hosted solution by ChemAxon? Is the software cloud-ready?

      Yes, ChemAxon can provide the necessary hardware and software for using Plexus Suite as a hosted solution, with the help of, for instance, Amazon's cloud services.

    Plexus Connect Plexus Connect is the backbone of Plexus Suite, which includes database management and chemical search functions through tables and forms. What is Plexus Connect?

    • What can I use Plexus Connect for? You can share your chemical databases securely through the web with partners, collaborators, geographically separated teams, branches, with all of your employees, or simply with everyone.

    • Which licenses do I need for Plexus Suite in order to browse my Instant JChem database? As the core module in Plexus Suite, Plexus Connect offers data management, data browsing and search tools. It requires the Plexus Connect license along with the Marvin JS and Instant JChem Enterprise licenses. (These two are added automatically to your license file containing the Plexus Connect license.) The Instant JChem Enterprise license is required when you are using a remote database (such as Oracle, MySQL...), but Instant JChem also serves as an administrative tool for Plexus Suite. Migration from Instant JChem

    • What is the migration path from Instant JChem desktop to the Plexus Connect web application?

      Instant JChem is the administrative interface of Plexus Connect, hence using existing Instant JChem projects in Plexus Connect should work smoothly.

    • I already have Instant JChem. Can I publish my database and forms to the web?

      Yes, with Plexus Connect you can put your databases and existing Instant JChem forms on the web, and distribute them among your colleagues . Running Plexus Connect

    • How can I create new database views (forms or grids) for Plexus Suite?

      As an administrator, you can use the visual form designer of Instant JChem Enterprise to create new database views.

    • Can I connect to the same database from Plexus Connect and from Instant JChem?

      Yes, you can connect to the same database from both interfaces at the same time. You can even connect in administrator mode through Instant JChem while the Plexus Connect server is running. In this case, however, you have to make sure that you use a different user account for the Instant JChem login from the account which is used for running the Plexus Connect server.

    • Can I connect to more than one database schema at one time?

      You can connect to several schemas with Plexus Connect. In this case, each schema configuration file has to be placed in the ${HOME}/.instantjchem/ijcWebServer folder , where ${HOME} means the home directory of the user running the web server. You also have to make sure that every schema has the same security configuration.

    • Which chemical sketchers are supported in Plexus Suite?

      Currently, Plexus Suite supports only ChemAxon's Marvin JS editor. You can learn more about Marvin JS here. Upgrading Plexus Connect

    • How often do I need to update Plexus Suite, and what are the requirements?

      Just like with other products, ChemAxon releases a new version of Plexus Suite every week. Upgrading to a new version is optional, you can follow the new features added to Plexus Suite in our Plexus Suite History of Changes.

    • How can I update to the latest version?

      Please, install the latest version of Instant JChem and deploy the same version of Plexus Connect. A detailed deployment guide can be found here. Security in Plexus Connect

    • How can I control who can access the data?

      With role-based security you can control which user groups can see a given view or query. If you use an Oracle database backend, you can use row-level security as well to specify which records can be seen by certain users.

    • How can I add/import data into a Plexus database?

      Data manipulation (import, add, edit, delete etc.) can be performed only by administrators through Instant JChem that serves as an administrative interface for Plexus Connect.

    • Who can edit the database?

      At the moment, Plexus Connect is a read-only application, users can browse and search the data they have access to. Administrators register data, design forms, and maintain the database using the Instant JChem Enterprise application. Plexus Connect and Instant JChem Web Client

    • What is the difference between Instant JChem Web Client and Plexus Connect?

      Plexus Connect is ChemAxon's new generation software, and it fully replaces Instant JChem Web Client. In the future, Plexus Connect should be used instead of Instant JChem Web Client.

      Plexus Connect is the core module of Plexus Suite. For more information about Plexus Suite, please, visit our website, or check the Plexus Suite User's Guide.

      Beside migrating the complete feature set of Instant JChem Web Client into Plexus Connect, new functionality is being developed in it continuously. Furthermore, Plexus Connect can be extended with other Plexus modules, for instance, library enumeration can be used within the Plexus Design module.

    • I have an Instant JChem Web Client license. What can I do?

      Please note that Plexus Connect cannot be used with Instant JChem Web Client license. For this, you will need a Plexus Connect license and an Instant JChem Enterprise license as well, since Instant JChem serves as an administrative interface for Plexus Suite. If you want to use further Plexus Suite modules, e.g., Plexus Design, you will need a license for these modules as well. Troubleshooting

    • I cannot log in to Plexus Connect. What can I do?

      1. Make sure that you have the permissiong to access the schema.

      2. Open Instant JChem and connect to the schema in administrator mode. In the Schema Settings dialog, make sure that that the Connect schema automatically , Remember username and Remember password options are checked.

      3. The schema configuration file ( .ijs ) has to be put in its default location in the ${HOME}/.instantjchem/ijcWebServer folder, where ${HOME} means the home directory of the user running the web server. The schema configuration file has to contain the ijc.username and ijc.password properties, as well as the database.url. (Furthermore, in the case of a remote database, the database.username and database.password properties have to be added as well.) In addition, the ijc username and password has to belong to a user account which has administrator role assigned to it in Instant JChem.

    • What is the best way to report my issues or ask questions?

      Please, feel free to report to the Plexus Suite user forum, or send an email to

      We will answer your request within one business day.