Bioinformatics Resources at Penn: BioCyc Pathway/Genome Database Collection

BioCyc is a collection of more than 14,000 Pathway Genome Databases (PGDBs) along with tools that can be used to analyze them.

BioCyc contains:

• quality data that is curated from thousands of publications. 
• computationally predicted metabolic pathways and operons     
• data integrated from other databases including gene essentiality, regulatory networks, protein features, and GO annotations.             

Here is a compilation of some of the most Frequently Asked Questions on BioCyc that we have received so far.

• Is there a way to redirect the BLAST/comparative analysis results to my email if the connection to the server gets disconnected?
  • No
• Do you delete accounts once subscriptions expire?
  • No, subscriptions and accounts are independent- especially for institutional subscriptions. SRI doesn't have any policy in this area, and they don't routinely delete accounts. At some point BioCyc will be deleting accounts that have been inactive for years.         
• Will SmartTables that are associated to an inactive BioCyc account will eventually get removed from the list of public SmartTables?
  • No, BioCyc will definitely retain "published" SmartTables, and they may retain public SmartTables as well.
• If I require technical assistance who should I contact?
  • Please contact BioCyc via email at biocyc-support@ai.sri.com
• I have issues with logging into my BioCyc account. What should I do?
  • A representative at SRI will forward your email regarding the login issues to Phoenix Bioinformatics- a non-profit institution that collects BioCyc subscriptions on behalf of SRI International.
• Is there a way to access my BioCyc account off-campus?
  • Yes, you can access your account remotely via Franklin from Penn Libraries. You can search for "BioCyc" under 'databases' and click on 'Connect to full text'. You will then be prompted to enter your PennKey and from there you will be able to access the BioCyc homepage. You will now be able to log in with your credentials to access your BioCyc account . 
• Does SRI store search strategies and/or history of analyses?
  • No