SpatialAgent: An autonomous AI agent for spatial biology

 https://www.biorxiv.org/content/10.1101/2025.04.03.646459v1

https://aipipelines.xlabub.com/

 https://aipipelines.xlabub.com/

• Domain Name: xlabub.com

• Registry Domain ID: Unique ID assigned by the .com registry (VeriSign)

• Creation Date: January 20, 2024

• Updated Date: December 16, 2024 (last time registration details were changed)

• Expiration Date: January 20, 2026 (current registration term ends)

OpenSSF Best Practices Badge Program

 https://www.bestpractices.dev/en

The Open Source Security Foundation (OpenSSF) Best Practices badge is a way for Free/Libre and Open Source Software (FLOSS) projects to show that they follow best practices. Projects can voluntarily self-certify, at no cost, by using this web application to explain how they follow each best practice. The OpenSSF Best Practices Badge is inspired by the many badges available to projects on GitHub. Consumers of the badge can quickly assess which FLOSS projects are following best practices and as a result are more likely to produce higher-quality secure software.

You can easily see the criteria for the passing badge. Automated analysis will determine many of the criteria answers for you (and prevent obviously incorrect answers). More information on the OpenSSF Best Practices Badging program is available on GitHub. Project statistics and criteria statistics are available. The projects page shows participating projects and supports queries (e.g., you can see projects that have a passing badge). You can also see an example (where we try to earn our own badge). This project was formerly known as the Core Infrastructure Initiative (CII) Best Practices badge. and was originally developed under the CII. It is now part of the OpenSSF Best Practices Working Group (WG). The OpenSSF is a foundation of the Linux Foundation (LF). The project was formally renamed from "CII Best Practices badge" on 2021-12-24.

Privacy and legal issues: Please see our privacy policy, about cookies, and terms of use. The code for the badging application itself is released under the MIT license (projects pursuing a badge are under their respective licenses). All publicly-available non-code content managed by the badging application that was added or edited after 2024-08-23 is released under the Community Data License Agreement – Permissive, Version 2.0 (CDLA-Permissive-2.0). Previous contributions were licensed under either the Creative Commons Attribution License version 3.0 (CC-BY-3.0), or as CC-BY version 3.0 or later (CC-BY-3.0+). If referencing collectively or not otherwise noted, please credit the OpenSSF Best Practices badge contributors.

https://www.bestpractices.dev/en/criteria/0

FLOSS Best Practices Criteria (Passing Badge)

This is the set of best practices for Free/Libre and Open Source Software (FLOSS) projects to achieve the Open Source Security Foundation (OpenSSF) Best Practices passing badge. You can show this list with just the criteria or with additional information. The full set of criteria for all badge levels are also available.

See criteria discussion for more information about these criteria.

Passing

Basics

Basic project website content

• The project website MUST succinctly describe what the software does (what problem does it solve?). [description_good]
• The project website MUST provide information on how to: obtain, provide feedback (as bug reports or enhancements), and contribute to the software. [interact]
• The information on how to contribute MUST explain the contribution process (e.g., are pull requests used?) {Met URL} [contribution]
• The information on how to contribute SHOULD include the requirements for acceptable contributions (e.g., a reference to any required coding standard). {Met URL} [contribution_requirements]

FLOSS license

• The software produced by the project MUST be released as FLOSS. [floss_license]
• It is SUGGESTED that any required license(s) for the software produced by the project be approved by the Open Source Initiative (OSI). [floss_license_osi]
• The project MUST post the license(s) of its results in a standard location in their source repository. {Met URL} [license_location]

Documentation

• The project MUST provide basic documentation for the software produced by the project. {N/A justification} [documentation_basics]
• The project MUST provide reference documentation that describes the external interface (both input and output) of the software produced by the project. {N/A justification} [documentation_interface]

Other

• The project sites (website, repository, and download URLs) MUST support HTTPS using TLS. [sites_https]
• The project MUST have one or more mechanisms for discussion (including proposed changes and issues) that are searchable, allow messages and topics to be addressed by URL, enable new people to participate in some of the discussions, and do not require client-side installation of proprietary software. [discussion]
• The project SHOULD provide documentation in English and be able to accept bug reports and comments about code in English. [english]
• The project MUST be maintained. [maintained]

Change Control

Public version-controlled source repository

• The project MUST have a version-controlled source repository that is publicly readable and has a URL. [repo_public]
• The project's source repository MUST track what changes were made, who made the changes, and when the changes were made. [repo_track]
• To enable collaborative review, the project's source repository MUST include interim versions for review between releases; it MUST NOT include only final releases. [repo_interim]
• It is SUGGESTED that common distributed version control software be used (e.g., git) for the project's source repository. [repo_distributed]

Unique version numbering

• The project results MUST have a unique version identifier for each release intended to be used by users. [version_unique]
• It is SUGGESTED that the Semantic Versioning (SemVer) or Calendar Versioning (CalVer) version numbering format be used for releases. It is SUGGESTED that those who use CalVer include a micro level value. [version_semver]
• It is SUGGESTED that projects identify each release within their version control system. For example, it is SUGGESTED that those using git identify each release using git tags. [version_tags]

Release notes

• The project MUST provide, in each release, release notes that are a human-readable summary of major changes in that release to help users determine if they should upgrade and what the upgrade impact will be. The release notes MUST NOT be the raw output of a version control log (e.g., the "git log" command results are not release notes). Projects whose results are not intended for reuse in multiple locations (such as the software for a single website or service) AND employ continuous delivery MAY select "N/A". {N/A justification} {Met URL} [release_notes]
• The release notes MUST identify every publicly known run-time vulnerability fixed in this release that already had a CVE assignment or similar when the release was created. This criterion may be marked as not applicable (N/A) if users typically cannot practically update the software themselves (e.g., as is often true for kernel updates). This criterion applies only to the project results, not to its dependencies. If there are no release notes or there have been no publicly known vulnerabilities, choose N/A. {N/A justification} [release_notes_vulns]

Reporting

Bug-reporting process

• The project MUST provide a process for users to submit bug reports (e.g., using an issue tracker or a mailing list). {Met URL} [report_process]
• The project SHOULD use an issue tracker for tracking individual issues. [report_tracker]
• The project MUST acknowledge a majority of bug reports submitted in the last 2-12 months (inclusive); the response need not include a fix. [report_responses]
• The project SHOULD respond to a majority (>50%) of enhancement requests in the last 2-12 months (inclusive). [enhancement_responses]
• The project MUST have a publicly available archive for reports and responses for later searching. {Met URL} [report_archive]

Vulnerability report process

• The project MUST publish the process for reporting vulnerabilities on the project site. {Met URL} [vulnerability_report_process]
• If private vulnerability reports are supported, the project MUST include how to send the information in a way that is kept private. {N/A allowed} {Met URL} [vulnerability_report_private]
• The project's initial response time for any vulnerability report received in the last 6 months MUST be less than or equal to 14 days. {N/A allowed} [vulnerability_report_response]

Quality

Working build system

• If the software produced by the project requires building for use, the project MUST provide a working build system that can automatically rebuild the software from source code. {N/A allowed} [build]
• It is SUGGESTED that common tools be used for building the software. {N/A allowed} [build_common_tools]
• The project SHOULD be buildable using only FLOSS tools. {N/A allowed} [build_floss_tools]

Automated test suite

• The project MUST use at least one automated test suite that is publicly released as FLOSS (this test suite may be maintained as a separate FLOSS project). The project MUST clearly show or document how to run the test suite(s) (e.g., via a continuous integration (CI) script or via documentation in files such as BUILD.md, README.md, or CONTRIBUTING.md). [test]
• A test suite SHOULD be invocable in a standard way for that language. [test_invocation]
• It is SUGGESTED that the test suite cover most (or ideally all) the code branches, input fields, and functionality. [test_most]
• It is SUGGESTED that the project implement continuous integration (where new or changed code is frequently integrated into a central code repository and automated tests are run on the result). [test_continuous_integration]

New functionality testing

• The project MUST have a general policy (formal or not) that as major new functionality is added to the software produced by the project, tests of that functionality should be added to an automated test suite. [test_policy]
• The project MUST have evidence that the test_policy for adding tests has been adhered to in the most recent major changes to the software produced by the project. [tests_are_added]
• It is SUGGESTED that this policy on adding tests (see test_policy) be documented in the instructions for change proposals. [tests_documented_added]

Warning flags

• The project MUST enable one or more compiler warning flags, a "safe" language mode, or use a separate "linter" tool to look for code quality errors or common simple mistakes, if there is at least one FLOSS tool that can implement this criterion in the selected language. {N/A allowed} [warnings]
• The project MUST address warnings. {N/A allowed} [warnings_fixed]
• It is SUGGESTED that projects be maximally strict with warnings in the software produced by the project, where practical. {N/A allowed} [warnings_strict]

Security

Secure development knowledge

• The project MUST have at least one primary developer who knows how to design secure software. (See ‘details’ for the exact requirements.) [know_secure_design]
• At least one of the project's primary developers MUST know of common kinds of errors that lead to vulnerabilities in this kind of software, as well as at least one method to counter or mitigate each of them. [know_common_errors]

Use basic good cryptographic practices

• The software produced by the project MUST use, by default, only cryptographic protocols and algorithms that are publicly published and reviewed by experts (if cryptographic protocols and algorithms are used). {N/A allowed} [crypto_published]
• If the software produced by the project is an application or library, and its primary purpose is not to implement cryptography, then it SHOULD only call on software specifically designed to implement cryptographic functions; it SHOULD NOT re-implement its own. {N/A allowed} [crypto_call]
• All functionality in the software produced by the project that depends on cryptography MUST be implementable using FLOSS. {N/A allowed} [crypto_floss]
• The security mechanisms within the software produced by the project MUST use default keylengths that at least meet the NIST minimum requirements through the year 2030 (as stated in 2012). It MUST be possible to configure the software so that smaller keylengths are completely disabled. {N/A allowed} [crypto_keylength]
• The default security mechanisms within the software produced by the project MUST NOT depend on broken cryptographic algorithms (e.g., MD4, MD5, single DES, RC4, Dual_EC_DRBG), or use cipher modes that are inappropriate to the context, unless they are necessary to implement an interoperable protocol (where the protocol implemented is the most recent version of that standard broadly supported by the network ecosystem, that ecosystem requires the use of such an algorithm or mode, and that ecosystem does not offer any more secure alternative). The documentation MUST describe any relevant security risks and any known mitigations if these broken algorithms or modes are necessary for an interoperable protocol. {N/A allowed} [crypto_working]
• The default security mechanisms within the software produced by the project SHOULD NOT depend on cryptographic algorithms or modes with known serious weaknesses (e.g., the SHA-1 cryptographic hash algorithm or the CBC mode in SSH). {N/A allowed} [crypto_weaknesses]
• The security mechanisms within the software produced by the project SHOULD implement perfect forward secrecy for key agreement protocols so a session key derived from a set of long-term keys cannot be compromised if one of the long-term keys is compromised in the future. {N/A allowed} [crypto_pfs]
• If the software produced by the project causes the storing of passwords for authentication of external users, the passwords MUST be stored as iterated hashes with a per-user salt by using a key stretching (iterated) algorithm (e.g., Argon2id, Bcrypt, Scrypt, or PBKDF2). See also OWASP Password Storage Cheat Sheet. {N/A allowed} [crypto_password_storage]
• The security mechanisms within the software produced by the project MUST generate all cryptographic keys and nonces using a cryptographically secure random number generator, and MUST NOT do so using generators that are cryptographically insecure. {N/A allowed} [crypto_random]

Secured delivery against man-in-the-middle (MITM) attacks

• The project MUST use a delivery mechanism that counters MITM attacks. Using https or ssh+scp is acceptable. [delivery_mitm]
• A cryptographic hash (e.g., a sha1sum) MUST NOT be retrieved over http and used without checking for a cryptographic signature. [delivery_unsigned]

Publicly known vulnerabilities fixed

• There MUST be no unpatched vulnerabilities of medium or higher severity that have been publicly known for more than 60 days. [vulnerabilities_fixed_60_days]
• Projects SHOULD fix all critical vulnerabilities rapidly after they are reported. [vulnerabilities_critical_fixed]

Other security issues

• The public repositories MUST NOT leak a valid private credential (e.g., a working password or private key) that is intended to limit public access. [no_leaked_credentials]

Analysis

Static code analysis

• At least one static code analysis tool (beyond compiler warnings and "safe" language modes) MUST be applied to any proposed major production release of the software before its release, if there is at least one FLOSS tool that implements this criterion in the selected language. {N/A justification} {Met justification} [static_analysis]
• It is SUGGESTED that at least one of the static analysis tools used for the static_analysis criterion include rules or approaches to look for common vulnerabilities in the analyzed language or environment. {N/A allowed} [static_analysis_common_vulnerabilities]
• All medium and higher severity exploitable vulnerabilities discovered with static code analysis MUST be fixed in a timely way after they are confirmed. {N/A allowed} [static_analysis_fixed]
• It is SUGGESTED that static source code analysis occur on every commit or at least daily. {N/A allowed} [static_analysis_often]

Dynamic code analysis

• It is SUGGESTED that at least one dynamic analysis tool be applied to any proposed major production release of the software before its release. [dynamic_analysis]
• It is SUGGESTED that if the software produced by the project includes software written using a memory-unsafe language (e.g., C or C++), then at least one dynamic tool (e.g., a fuzzer or web application scanner) be routinely used in combination with a mechanism to detect memory safety problems such as buffer overwrites. If the project does not produce software written in a memory-unsafe language, choose "not applicable" (N/A). {N/A allowed} [dynamic_analysis_unsafe]
• It is SUGGESTED that the project use a configuration for at least some dynamic analysis (such as testing or fuzzing) which enables many assertions. In many cases these assertions should not be enabled in production builds. [dynamic_analysis_enable_assertions]
• All medium and higher severity exploitable vulnerabilities discovered with dynamic code analysis MUST be fixed in a timely way after they are confirmed. {N/A allowed} [dynamic_analysis_fixed]

safe ose FAQ

safe ose FAQ 

https://www.nsf.gov/pubs/2025/nsf25027/nsf25027.jsp

R universe

 https://ropensci.org/blog/2021/06/22/setup-runiverse/

https://ropensci.org/blog/2023/04/03/cran-to-git/

Tougaloo College

 Tougaloo College, a historically Black college in Mississippi, is actively involved in public health research and education, often collaborating with other institutions. Below are some highlights related to Tougaloo's public health initiatives and connections to Alabama:

• Collaborations in Public Health Research: Tougaloo College has a longstanding partnership with Brown University. Recently, students from both institutions studied the community health impacts of a wood pellet manufacturing plant in rural Mississippi. This research focused on rural public health challenges and was presented to community members and at health conferences1.

• Health Disparities Research: Wendy White, a researcher associated with Tougaloo College, serves as the Principal Investigator for the Jackson Heart Study Undergraduate Training and Education Center. Her work focuses on health disparities research and mentoring students in public health careers2.

• Training Programs: Tougaloo College participates in initiatives like the UCLA-Tougaloo Public Health Scholars Training Program, which helps students develop research skills by working with faculty on projects such as data collection and manuscript preparation3.

• Connections to Alabama: While there is no direct mention of a Tougaloo researcher specifically based in Alabama, there are ties between Tougaloo's public health efforts and broader regional collaborations. For example, Alabama institutions like the University of Alabama at Birmingham (UAB) are also heavily involved in public health research, including health disparities5.

ODU storage managment

 

https://itsapps.odu.edu/apps/web/research_storage_options/

Research Storage Matrix

Before using an IT service to compute large amounts of confidential or restricted data, be sure you are using the right computing environment for the job.

According to ITS Standard 02.3.0, there are five classification levels of data that require different levels of protection. ODU has several research computing environments, each with its own strengths and/or limitations where sensitive data is concerned. The matrix below lists the environments best suited to the type of data you collect as part of your research, based on your data’s classification level. Definitions of each class can be found in the footnotes.

Keep in mind, these are just guidelines. Contact the Office of Research Compliance and the ITS Information Security Officer to discuss your specific research circumstances.

How to access research computing environments

For access to HPC, CCI-R, ACCORD and Redcap, contact ITSResearchandCloudComputing@odu.edu.
For access to RRCE and MUSA, contact dflanaga@odu.edu.

How to interpret the Regulated Research Data Matrix

   Acceptable It is ok to use this environment with data in this category.
   Not Appropriate This environment is not equipped to handle this type of regulated data. Do not use this environment with data in this category.

  Public Data  Confidential Data  Restricted Data 

	Public Data	Confidential Data		Restricted Data
Data Types	Non-Sensitive & Public Data5	Confidential: Intellectual Property3 (unregulated)	FERPA2,3	PHI1,2,3,*, EAR2,3	IPI1,2,3,†	HIPAA1	CUI1,‡/ITAR1,2	Classified
OneDrive for Business An enterprise service that allows users to store, share and edit files within online Office apps as part of Microsoft Office 365.		b	b
Microsoft Teams/SharePoint An online collaboration space that is part of Office 365.		a,b	a
HPC HPC clusters offer substantial computational power to critical research projects in disciplines including cybersecurity, resilience and data-intensive science and engineering.
CCI-R COVA CCI is southeastern Virginia's engine for research, innovation, and commercialization of next-generation cybersecurity technologies particularly in the areas of Cyber Physical Systems Security (CPSS), 5G, and Artificial Intelligence (AI) in the Maritime, Defense, and Transportation industries.
RRCE The Regulated Research Computational Environment (RRCE) is built through a partnership between ODU, EVMS and Sentara. It provides a virtual lab environment for computation and storage of regulated data sets including CUI and HIPAA.
ACCORD
MUSA
REDCap Research Electronic Data Capture (REDCap) is a web-based application is HIPAA–compliant, highly secure, and intuitive to use.

Legend

1	Class 1: Restricted (most sensitive; Examples: SSN, Driver’s License number, PHI, HIPAA, CUI, ITAR)
2	Class 2: Confidential, Moderate Sensitivity (non-restricted data regulated by state/federal laws; Examples: Human genomic data, FERPA non-directory data, EAR)
3	Class 3: Confidential, Low Sensitivity (Examples: FERPA directory data, intellectual properties)
4	Class 4: Confidential, Non-Regulated (Examples: non-public, non-regulated research data)
5	Class 5: Public
*	PHI is always classified level 1, unless it is de-identified for research purposes, in which case it could be classified at level 2 or 3, depending on data requirements and agreements.
†	IPI (Identifiable Private Information) is private information for which the identity of the subject is or may readily be ascertained by the investigator or is associated with the information. See more: Coded Private Information or Biospecimens Used in Research | HHS.gov
a	a In restricted folders with access limited to only ODU employees who have a need to know.
b	Temporary files or working copies that are non-authoritative and not source documents.