{"id":18669986,"url":"https://github.com/blahah/phd","last_synced_at":"2025-06-12T22:03:27.570Z","repository":{"id":66276028,"uuid":"45273958","full_name":"blahah/phd","owner":"blahah","description":"My phd thesis (WIP)","archived":false,"fork":false,"pushed_at":"2017-05-04T22:01:51.000Z","size":5127,"stargazers_count":9,"open_issues_count":10,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-05-18T08:35:21.738Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"http://rik.smith-unna.com/phd/thesis.html","language":"TeX","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/blahah.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2015-10-30T20:05:09.000Z","updated_at":"2021-01-24T18:57:45.000Z","dependencies_parsed_at":null,"dependency_job_id":"712c404b-fcb6-45d5-bb78-0bb102d326be","html_url":"https://github.com/blahah/phd","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/blahah/phd","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/blahah%2Fphd","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/blahah%2Fphd/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/blahah%2Fphd/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/blahah%2Fphd/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/blahah","download_url":"https://codeload.github.com/blahah/phd/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/blahah%2Fphd/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":259539025,"owners_count":22873332,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-07T08:49:24.439Z","updated_at":"2025-06-12T22:03:27.534Z","avatar_url":"https://github.com/blahah.png","language":"TeX","funding_links":[],"categories":[],"sub_categories":[],"readme":"## PhD thesis\n\nThis is my PhD thesis. It's a work in progress.\n\nYou can see the HTML version of something like the current state here: http://rik.smith-unna.com/phd/thesis.html\n\nWorking title:\n\n**A phylotranscriptomic reasoning framework for C4 photosynthesis research.**\n\nExpected structure:\n\n1. Introduction\n2. Measuring transcriptome assemblies\n3. In pursuit of the optimal transcriptome assembly\n4. Building high-quality transcriptomic resources for C4 research\n5. Reasoning about C4 with a phylogenetically structured model\n6. [if time] Updating our beliefs about C4 with old and new data\n\nNote: It may not compile cleanly while it's a WIP. I'll make releases as each chapter is done/drafted.\n\n## Contributing\n\nI'm putting work here *as I write it*. People often seem afraid to do this, but I make mistaked like everyone else (edit: see!), and I'm happy with that.\n\nIf you feel like reading the work, I'd love to hear what you think. Comments, questions, suggestions, and pointing out mistakes, stupidity or anything else, are all welcome! Please create an issue. Or email me (rds45\u003cat\u003ecam.ac.uk) if you'd prefer to talk in private (though I'm happy to be called out in public).\n\n## Installing pre-requisites\n\nYou'll need:\n\n- `pandoc`\n- `pandoc-fignos`\n- `pandoc-eqnos`\n- a LaTeX distribution\n\ne.g. on OSX:\n\nFirst install MacTeX from: https://www.tug.org/mactex/\n\nThen with homebrew:\n\n```bash\nbrew install pandoc\npip install pandoc-fignos pandoc-eqnos\n```\n\n## Making the thesis\n\n```bash\nmake html\n# OR\nmake pdf\n# OR\nmake # for both PDF and HTML\n```\n\n## Building figures from scratch\n\n```bash\nmake figureimg\n```\n\n### Pre-requisites\n\n- [`mermaid`](https://github.com/knsv/mermaid) for flow-charts\n- `node.js` for mermaid\n- `mmv`\n\ne.g. on OSX:\n\n```bash\n# install node.js\nwget -qO- https://raw.githubusercontent.com/creationix/nvm/v0.29.0/install.sh | bash\nnvm install 5.0.0\n# install mermaid\nnpm install --global mermaid phantomjs\n# install mmv\nbrew install mmv\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fblahah%2Fphd","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fblahah%2Fphd","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fblahah%2Fphd/lists"}