[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"doc-detail-85045-en":3,"doc-seo-85045-105":29,"detail-sidebar-cat-0-en-105":82},{"code":4,"msg":5,"data":6},0,"success",{"doc_id":7,"user_id":8,"nickname":9,"user_avatar":10,"doc_module":4,"category_id":11,"category_name":12,"doc_title":13,"doc_description":14,"doc_content":15,"file_id":16,"file_url":17,"file_type":18,"file_size":19,"view_count":20,"is_deleted":4,"is_public":21,"is_downloadable":21,"audit_status":21,"page_count":11,"language":22,"language_code":23,"site_id":24,"html_lang":23,"table_of_contents":25,"faqs":26,"seo_title":13,"seo_description":14,"update_tm":27,"read_time":28},85045,1099514067415,"Rowan","https://ap-avatar.wpscdn.com/avatar/100002539d78ffe74a7?x-image-process=image/resize,m_fixed,w_180,h_180&k=1779092875211072502",8,"Research & Report","Aleena Alignment Agent for Research Software Engineering Collaborations","Research software collaborations span meetings, informal chats, pull requests, and GitHub issues, where decisions can lose their original rationale across artifacts, fragmenting shared understanding of intent, ownership, and scientific assumptions. The work argues alignment in research software engineering is a continuous lifecycle challenge and that agentic AI can assist stakeholder alignment and project-state tracking without replacing human judgment. It introduces Aleena, an open-source lifecycle alignment agent using GitHub to convert multimodal interactions into structured project records that surface risks, track open questions, and preserve decision continuity.","Aleena: Alignment Agent for Research Software Engineering  \nCollaborations  \nKshitij Dani  \neScience Institute University of Washington Seattle, Washington, USA [ksdani@uw.edu](ksdani@uw.edu)  \nCordero Core  \neScience Institute University of Washington Seattle, Washington, USA [cdcore@uw.edu](cdcore@uw.edu)  \nLandung Setiawan  \neScience Institute University of Washington Seattle, Washington, USA[landungs@uw.edu](landungs@uw.edu)  \nCarlos Garcia Jurado Suarez  \neScience Institute University of Washington Seattle, Washington, USA [carlosg@uw.edu](carlosg@uw.edu)  \nAnshul Tambay  \neScience Institute University of Washington Seattle, Washington, USA [anshul37@uw.edu](anshul37@uw.edu)  \nVani Mandava  \neScience Institute University of Washington Seattle, Washington, USA [vani1@uw.edu](vani1@uw.edu)  \narXiv :2607 .08043v 1 [ cs . SE] 9 Jul 2026  \nAnant Mittal  \neScience Institute University of Washington Seattle, Washington, USA [anmittal@uw.edu](anmittal@uw.edu)  \nAbstract  \nResearch software collaborations span meetings, informal chats, pull requests, and GitHub issues. A decision surfaced in a Slack thread, refined in a meeting, and implemented in a pull request can lose its original rationale across these artifacts, leaving domain researchers and research software engineers with divergent mental models of project intent, ownership, and scientific assumptions. We argue that alignment in research software engineering is a continuous lifecycle problem, and that agentic AI can supportstakeholder alignment and project-state tracking without replacing human decision-making. We present Aleena, an open-source lifecycle alignment agent that uses GitHub as a shared collaboration surface, transforming multi-modal stakeholder interactions into structured project records that surface risks, track open questions, and preserve decision continuity. Grounded in university-based research software engineering center experiences, this paper presents the motivating problem, system design, prototype, and illustrative lifecycle scenarios for Aleena.  \n1 Introduction  \nResearch software collaborations play a central role in advancing science by supporting researchers to translate domain-specific goals, workflows, and computational methods into usable software systems. Yet this software begins as research prototypes that prioritize scientific results over engineering practice, and is written by scientists with limited training in software engineering [1, 8, 17, 19, 20, 24, 26, 34, 42] . Compounding this gap, such collaborations operate under evolving scope and incomplete requirements: scientific software developers rarely produce formal requirements documents, because requirements emerge as both the software and the researcher’s understanding of the domain mature [4] .  \nIn practice, project context is distributed across interaction modalities that are central coordination mechanisms in  \nsoftware engineering teams, including synchronous meetings, asynchronous chats (e.g., Slack or Teams), email threads, and design discussions [49] . It is further distributed across collaboration platforms such as GitHub, where issues, pull requests, and discussions carry overlapping but partial fragments of project history [16, 18, 50]. Across these surfaces, two directions of teaching occur in parallel: researchers teach engineers the scientific domain (e.g., data semantics, valid input ranges, modeling assumptions, domain conventions), while engineers teach researchers software practices (e.g., version control, testing, continuous integration, deployment, reproducibility), a translation that depends on boundary objects that travel between communities of practice while preserving meaning on each side [30, 45] . For mature projects, this distributed context also accumulates legacy decisions, prior design tradeoffs, and rationale behind historical technical choices.  \nThe consequence is a persistent alignment challenge. Researchers describe needs in domain-specific vocab","cbCairIT1V6xLfaW","https://ap.wps.com/l/cbCairIT1V6xLfaW","pdf",1504259,2,1,"English","en",105,"# Introduction\n## Collaboration and distributed project context\n## Persistent alignment challenge\n## Research software engineering centers and observed issues\n# Aleena: lifecycle alignment agent\n## GitHub-based shared collaboration surface\n## Multimodal artifact transformation and outputs","[{\"question\":\"How does Aleena use GitHub to support alignment?\",\"answer\":\"Aleena treats GitHub as a central collaboration surface and operates across multimodal artifacts such as meeting/chat transcripts, issues, discussions, and pull requests. The prototype transforms submitted artifacts into structured summaries, risks, open questions, and suggestions to maintain decision continuity.\"}]",1784200598,20,{"code":4,"msg":30,"data":31},"ok",{"site_id":24,"language":23,"slug":32,"title":13,"keywords":33,"description":14,"schema_data":34,"social_meta":77,"head_meta":79,"extra_data":81,"updated_unix":27},"aleena-alignment-agent-for-research-software-engineering-collaborations","",{"@graph":35,"@context":76},[36,52,67],{"@type":37,"itemListElement":38},"BreadcrumbList",[39,43,46,49],{"item":40,"name":41,"@type":42,"position":21},"https://docshare.wps.com","Home","ListItem",{"item":44,"name":45,"@type":42,"position":20},"https://docshare.wps.com/document/","Document",{"item":47,"name":12,"@type":42,"position":48},"https://docshare.wps.com/document/research-report/",3,{"item":50,"name":13,"@type":42,"position":51},"https://docshare.wps.com/document/aleena-alignment-agent-for-research-software-engineering-collaborations/85045/",4,{"url":50,"name":13,"@type":53,"author":54,"headline":13,"publisher":56,"fileFormat":59,"inLanguage":23,"description":14,"dateModified":60,"datePublished":61,"encodingFormat":59,"isAccessibleForFree":62,"interactionStatistic":63},"DigitalDocument",{"name":9,"@type":55},"Person",{"url":40,"name":57,"@type":58},"DocShare","Organization","application/pdf","2026-07-24","2026-07-16",true,{"@type":64,"interactionType":65,"userInteractionCount":20},"InteractionCounter",{"@type":66},"ViewAction",{"@type":68,"mainEntity":69},"FAQPage",[70],{"name":71,"@type":72,"acceptedAnswer":73},"How does Aleena use GitHub to support alignment?","Question",{"text":74,"@type":75},"Aleena treats GitHub as a central collaboration surface and operates across multimodal artifacts such as meeting/chat transcripts, issues, discussions, and pull requests. 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