readme and .gitignore updated

.gitignore

@@ -0,0 +1,44 @@
+
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+# Unit test / coverage reports
+.tox/
+.coverage
+.cache
+nosetests.xml
+coverage.xml
+# Translations
+*.mo
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+# Rope
+.ropeproject
+# Django stuff:
+*.log
+*.pot
+# Sphinx documentation
+# docs/_build/
+
+
+.vscode
+.venvs
+deprecated/
+data/
+notes/
+pyDNA_EPBD/
+tune_EPBD_crossattn/
+resources*
+epbd_bert/dnabert2_epbd_crossattn/outputs
+analysis/data
+analysis_motif_discovery/data
+**/__pycache__/

README.md

@@ -26,9 +26,9 @@ and the effectiveness of multi-modal deep learning models in gene regulation stu
 ## Resources
 
 - [Paper](https://www.biorxiv.org/content/10.1101/2024.01.16.575935v2.abstract)
-- [Code](https://github.com/ceodspspectrum/EPBD-BERT)
-- [Documentation](https://github.io/ceodspspectrum/EPBD-BERT)
-- [Analysis Notebooks](https://github.com/ceodspspectrum/EPBD-BERT/tree/main/analysis)
+- [Code](https://github.com/lanl/EPBD-BERT)
+- [Documentation](https://lanl.github.io/EPBD-BERT/)
+- [Analysis Notebooks](https://github.com/lanl/EPBD-BERT/tree/main/analysis)
 
 ## Installation