Note: This is not a legal document or contract. This document attempts to describe guidelines for proper user behavior on the Secondary Metabolism Collaboratory (SMC). # About SMC and its Code of Conduct The goal of SMC is to create an environment for exploration, discovery, and the sharing of scientific data on natural product biosynthetic gene clusters. The SMC web platform, as well as its associated user-available APIs, makes it possible to discuss scientific data, introduce new data, and generally make comments that are publicly visible. The purpose of this is to facilitate open scientific discussions, and to connect our users to one another to build a vibrant, engaged community. As with all scientific inquiry, we expect that debate and healthy argument will be a common occurrence. ***Our first and primary expectation is that all users of SMC will participate in discourse with kindness, respect, responsibility, professionalism, and rigorous scientific ethics.*** Through the SMC’s platforms, the DOE Joint Genome Institute (JGI) is committed to providing a welcoming, harassment-free experience for all users, and to facilitate this, we expect our users to abide by certain community standards, articulated here. This policy is a work in progress. At this time, this policy lives as an editable Google document. Please add comments or suggestions with the “Add Comment” tool. # Data Usage Policy and Data Privacy Users may assume that all data hosted on the SMC database, delivered via its API, and served through its web frontend, is freely available without restriction. SMC’s data is generated with open software from the scientific community run on freely-available sequence data, and therefore we believe that we cannot, nor should, place restrictions on its use. Further, as a “collaboratory”, the site aims to allow users to upload novel data, make improvements to data, and link to outside servers and information sources. We believe that building a community like this requires trust, accountability, and minimal anonymity. If you choose to use the website, database, or API, you should be aware that: * User activity (data uploads, commentary, file access) is tracked and stored * Most data may be accessed anonymously (in that a user need not be logged in to the SMC/JGI login system), but users must be logged in to use comment, upload, or API access features. * The system may announce your activities, including your system-provided name or username, on the SMC homepage. Your username will also be attached to your comments, and to your annotations * Website usage and access is tracked using common website traffic analysis tools, and may log your IP address or keep other logs of your activity on our servers for analysis purposes Users are free to register a JGI account with a false name, to preserve personal privacy, but we strongly encourage you to be a part of the established scientific community. Our hope is that SMC will be a central online collaborative hub for genome mining, and we all want to know who you are and hope to watch your career grow\! Further, ALL data uploaded to SMC, whether by automated systems or by users, is viewable to the public, and we (purposely) do not have systems in place to keep your data secret, and, thus, we cannot and will not take the responsibility to restrict its access or use by the rest of the scientific community. ***If you wish your data to remain private, do not upload it to SMC or its systems.*** Generally, the term “upload” may refer to deposition of source (ie genome, metagenome, contig, etc) sequences, creation of comments made to source or BGC webpages, deposition of unique BGC annotations, or any other methods that allow one to place data in the system via the website or the API. In most cases your data is editable or may be deleted by you, while you are logged into the system. ***Unauthorized uploading of unpublished, embargoed, restricted, or otherwise private data is a violation*** of the SMC Code of Conduct (see “Scientific Misconduct”, below), and in such cases the data will be removed when discovered or reported, and the violating user may lose login privileges. If you have mistakenly uploaded data that does not belong on the system for any reason, in most cases a site moderator is empowered to remove it. To resolve issues like this, please contact a moderator via the [contact form](https://smc.jgi.lbl.gov/contact-us). Regarding personally-identifiable data and GDPR compliance: At this time SMC and JGI make no claims for or counter to GDPR compliance. However, we do expect that SMC is compliant, and EU users should know that: * The only personal data SMC collects and stores is the email address and name supplied to JGI’s ORCID-based Single Sign-On system, which is strictly used for associating a user’s posts to the poster, privilege levels, and for supplying API access tokens. * SMC does not conduct analytics on individual users or their usage patterns, profile individual users, or conduct location-based analytics, and there are no mechanisms in place to store such data within SMC or its systems. * SMC and JGI will never sell or pass any personal user information to any third party * SMC and JGI do not use any third party cookies * Any data posted to SMC by a user is strictly voluntary, and can be deleted by the poster using APIs or the web interface. User accounts and associated data can be deleted by a moderator upon request. Please make this request via the [contact form](https://smc.jgi.lbl.gov/contact-us). # Expectations of User Conduct As with any open communications tool, we recognize that it is possible that users might communicate in undesirable or inappropriate ways, which may come in the form of harassment, intolerance and disrespect, scientific misconduct, or unwanted commercial advertisement. ***This behavior will not be tolerated.*** If anyone engages in inappropriate behavior on SMC’s platforms, then SMC moderators, JGI, and Lawrence Berkeley National Laboratory (Berkeley Lab) reserve the right to take any or all of the following actions, at their discretion: * warning the offender * removing, editing, or hiding the offending communications and/or data * removing the offender’s ability to post or upload data or otherwise engage with the SMC community * removing access to the SMC’s platforms * reporting offenses to the offender’s PI, workplace supervisor, and/or home institution or mother. * seeking help from law enforcement Forms of inappropriate behavior are defined in more detail below: ### Harassment We do not tolerate harassment in any form. Refrain from demeaning, discriminatory, or harassing behavior and speech. Harassment includes, but is not limited to: * offensive comments related to gender, gender identity and expression, age, sexual orientation, disability, physical appearance, body size, race, ethnicity, religion (or lack thereof), or technology choices * unwelcome comments regarding a person’s lifestyle choices and practices, including those related to food, health, parenting, drugs, or employment * unwelcome comments regarding a person’s educational level and/or institutional affiliations * sustained or willful disruption of a user’s comments or other contributions to the website * deliberate intimidation * continued one-on-one communication after requests to cease. This may include communications within the SMC’s platforms, or outside * threats of violence or incitement of violence towards any individual, including encouraging a person to commit suicide or to engage in self-harm * use of sexual or discriminatory imagery, comments, or jokes * unwelcome sexual attention * deliberate ‘outing’ of any aspect of a person’s identity without their consent except as necessary to protect vulnerable people from intentional abuse * deliberate misgendering or use of ‘dead’ or rejected names * publication of non-harassing private communication ### Intolerance and Disrespect In certain cases, intolerant or disrespectful communications will not rise to the level of harassment, but may still be seen as Code of Conduct violations. Common examples include excessive use of profanity, or angry or confrontational communications. Everyone who joins and participates in SMC must be treated with tolerance and respect, and all users shall conduct themselves with professionalism. ### Scientific Misconduct We do not tolerate scientific misconduct. We recognize that it is plausible and likely for users to make mistakes and communicate information later found to be untrue. This is normal to the scientific process, and is not misconduct if communicated in good faith. Scientific misconduct, rather, includes but is not limited to: * Fabrication of sequence data, annotation data, or any other data stored on or linked to SMC * Deliberate, knowing communication of fabricated, falsified, or manipulated data * Plagiarism, or duplicating works created by others without attribution * Sharing of unpublished, embargoed, restricted, or otherwise private data without the original authors’ permission * Creating false user identities, especially when employed for the purpose of anonymously promoting theories/work/data or for critiquing others’ theories/work/data ### Unrelated or Excessive Commercial Advertisements Secondary metabolism and natural products have a long, successful history in drug discovery and commercial use, and we welcome contributions from industry users in the form of services and products, if relevant to the context of a discussion. However, we do not view SMC as a venue for unsolicited and unrelated commercial advertisement. Any commercial offerings: * Must be directly relevant to the discussion in which they are posted * Must be posted as plain text or a hyperlink, and may not be posted in the form of images, animations, video, audio, or other nuisances * Must be posted by a registered user, and may not be automated * May not be posted more than once within a given conversation * Must not be excessive in length, and should be kept under 300 characters in length. ## What to do if you witness a violation, and what happens next User-posted comments that violate the Code Of Conduct above should first be “Flagged”, by pressing the flag icon on the comment, and then confirming by clicking “Yes” on the dialog box that appears. The system will immediately alert a moderator, who will personally evaluate the comment or posting, and may hide, edit, or delete the comment if it violates our policy, and may also remove a user’s ability to post or upload data at the moderator’s discretion, and/or take more severe corrective actions, if deemed warranted. If the violation is not related to a specific user-generated comment, we ask that you use the [contact form](https://smc.jgi.lbl.gov/contact-us), which can be found on the main SMC homepage through the “Contact Us” link in the “Help” menu section, as well as in the footer at the bottom of the page. Please provide links and any relevant information so that we can adequately evaluate the problem. In (hopefully) extremely rare instances, SMC moderators may seek advice from outside experts or neutral parties. ## Acknowledgements Portions of this Code of Conduct were inspired by, and some language regarding harassment adapted from, the [rOpenSci Code of Conduct version 2.2](https://ropensci.org/code-of-conduct/), and guidance from the University of California.