{"id":16499498,"url":"https://github.com/marcom/dss-opt","last_synced_at":"2026-05-13T00:03:29.047Z","repository":{"id":59866337,"uuid":"4927214","full_name":"marcom/dss-opt","owner":"marcom","description":"Dynamics in sequence space optimisation for RNA sequence design","archived":false,"fork":false,"pushed_at":"2023-08-01T11:28:31.000Z","size":200,"stargazers_count":3,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-01-12T09:23:41.738Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"C","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/marcom.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"COPYING","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":"2012-07-06T15:48:45.000Z","updated_at":"2024-02-08T08:37:46.000Z","dependencies_parsed_at":"2024-11-13T06:00:16.637Z","dependency_job_id":null,"html_url":"https://github.com/marcom/dss-opt","commit_stats":null,"previous_names":[],"tags_count":7,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/marcom%2Fdss-opt","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/marcom%2Fdss-opt/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/marcom%2Fdss-opt/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/marcom%2Fdss-opt/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/marcom","download_url":"https://codeload.github.com/marcom/dss-opt/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":241405079,"owners_count":19957764,"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":"2024-10-11T14:53:10.979Z","updated_at":"2026-05-13T00:03:29.020Z","avatar_url":"https://github.com/marcom.png","language":"C","funding_links":[],"categories":[],"sub_categories":[],"readme":"# dss-opt: Dynamics in Sequence Space Optimisation\n\nRNA sequence design for a given target secondary structure.  Sequences\nare designed by optimising a design score in a continuous sequence\nspace, allowing a mixture of bases at each position during\noptimisation.\n\n## Citation\n\nMarco C. Matthies, Stefan Bienert, Andrew E. Torda. Dynamics in\nSequence Space for RNA Secondary Structure Design. J. Chem. Theory\nComput., 2012, 8, 10, 3663--3670.\nhttps://doi.org/10.1021/ct300267j\n\n## Running the program\n\nThe dynamics in sequence space optimisation is performed with the program `opt-md`.\nThe `opt-sd` and `opt-sd-gsl` programs perform sequence design by gradient descent alone\nand are not described in the paper.\n```\n# show command-line arguments\n./opt-md -h\n\n# design a sequence for the target structure ((((...))))\n./opt-md '((((...))))'\n\n# you can often improve the quality of designed sequences by playing with\n# the --kneg and --khet parameters, which change the weights of the negative\n# design and sequence heterogeneity terms, as well as other parameters\n```\n\n## Build instructions\n\nThe code can be compiled by running `make` in this directory. You need\nthe GSL (GNU Scientific Library) header files and library installed\n(`libgsl-dev` package in Ubuntu).\n\nAdditionally, there is a little utility program called\n`rna-ensemble-distance` that uses the ViennaRNA library to compute the\ntarget probability and ensemble defect of a designed sequence with\nrespect to a given target structure.  You can find it in the\n`rna-ensemble-distance-with-ViennaRNA/` directory. The README file in\nthe\n[rna-ensemble-distance-with-ViennaRNA/](./rna-ensemble-distance-with-ViennaRNA/)\ndirectory contains instructions on how to build this utility.\n\n\n## Python interface\n\nThe beginnings of a python interface can be found in the directory\n`python/`.  Install it with\n```sh\npip install python/\n\n# alternatively, if you want to run the python unit tests, do\npip install python/[test]\n# run the python unit tests\npytest\n```\n\nExample usage:\n```python\nimport dssopt\ndssopt.opt_md('(((...)))')\n```\n\n\n## Energy parameters\n\nThe parameters for the RNA nearest neighbour energy model were\nconverted from ViennaRNA, many thanks to them.  The parameters were\nconverted from the ViennaRNA-1.8.5 `param/vienna17.par` parameter file\nto C code with `scripts/vienna_parse_param.py`. The generated C code\ncontaining the parameters can be found in `nn_param.c`.\n\n## Copyright and license\n\nAll code was written by Marco Matthies, Centre for Bioinformatics,\nHamburg and is licensed under the GNU General Public License, version\n3 or later.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmarcom%2Fdss-opt","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmarcom%2Fdss-opt","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmarcom%2Fdss-opt/lists"}