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@@ -9,7 +9,7 @@ This repository corresponds to the article titled **"Advancing Transcription Fac | |
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| .. figure:: ../../plots/EPBD_Arch.jpg | ||
| :width: 50% | ||
| :width: 70% | ||
| :align: center | ||
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| Figure 1: Overview of the proposed EPBDxBERT framework. | ||
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@@ -38,6 +38,26 @@ Resources | |
| * `Analysis Notebooks <https://github.com/lanl/EPBD-BERT/tree/main/analysis>`_ | ||
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| Installation | ||
| ======================================== | ||
| .. code-block:: shell | ||
| # Installation of virtural environment | ||
| git clone https://github.com/lanl/EPBD-BERT.git | ||
| cd EPBD-BERT | ||
| conda create -c conda-forge -p .venvs/epbd_bert_condavenv_test1 python=3.11 -y | ||
| conda activate .venvs/epbd_bert_condavenv_test1 | ||
| python setup.py install | ||
| conda install -c conda-forge scikit-learn scipy -y | ||
| pip uninstall triton # We did not utilize triton for underlying hardware dependency | ||
| # To deactivate and remove the venv | ||
| conda deactivate | ||
| conda remove --name epbd_bert_condavenv_test1 --all -y | ||
| conda remove -p .venvs/epbd_bert_condavenv_test1 --all -y | ||
| Acknowledgements | ||
| ======================================== | ||
| Los Alamos National Lab (LANL), T-1 | ||
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@@ -90,17 +110,23 @@ Authors | |
| - `Anny Usheva <mailto:Anny\_[email protected]>`_: Surgery, Rhode Island Hospital and Brown University | ||
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| How to cite EPBD-BERT? | ||
| ================== | ||
| ======================================== | ||
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| .. code-block:: console | ||
| @article{kabir2024advancing, | ||
| title = {Advancing Transcription Factor Binding Site Prediction Using DNA Breathing Dynamics and Sequence Transformers via Cross Attention}, | ||
| author = {Kabir, Anowarul and Bhattarai, Manish and Rasmussen, Kim {\O} and Shehu, Amarda and Bishop, Alan R and Alexandrov, Boian and Usheva, Anny}, | ||
| journal = {bioRxiv}, | ||
| pages = {2024--01}, | ||
| year = {2024}, | ||
| publisher = {Cold Spring Harbor Laboratory} | ||
| title = {Advancing Transcription Factor Binding Site Prediction Using DNA Breathing Dynamics and Sequence Transformers via Cross Attention}, | ||
| author = {Kabir, Anowarul and | ||
| Bhattarai, Manish and | ||
| Rasmussen, Kim {\O} and | ||
| Shehu, Amarda and | ||
| Bishop, Alan R and | ||
| Alexandrov, Boian and | ||
| Usheva, Anny}, | ||
| journal = {bioRxiv}, | ||
| pages = {2024--01}, | ||
| year = {2024}, | ||
| publisher= {Cold Spring Harbor Laboratory} | ||
| doi = {10.5281/zenodo.11130474}, | ||
| url = {https://www.biorxiv.org/content/10.1101/2024.01.16.575935v2} | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -9,7 +9,7 @@ This repository corresponds to the article titled **"Advancing Transcription Fac | |
|
|
||
|
|
||
| .. figure:: ../../plots/EPBD_Arch.jpg | ||
| :width: 50% | ||
| :width: 70% | ||
| :align: center | ||
|
|
||
| Figure 1: Overview of the proposed EPBDxBERT framework. | ||
|
|
@@ -38,6 +38,26 @@ Resources | |
| * `Analysis Notebooks <https://github.com/lanl/EPBD-BERT/tree/main/analysis>`_ | ||
|
|
||
|
|
||
| Installation | ||
| ======================================== | ||
| .. code-block:: shell | ||
| # Installation of virtural environment | ||
| git clone https://github.com/lanl/EPBD-BERT.git | ||
| cd EPBD-BERT | ||
| conda create -c conda-forge -p .venvs/epbd_bert_condavenv_test1 python=3.11 -y | ||
| conda activate .venvs/epbd_bert_condavenv_test1 | ||
| python setup.py install | ||
| conda install -c conda-forge scikit-learn scipy -y | ||
| pip uninstall triton # We did not utilize triton for underlying hardware dependency | ||
| # To deactivate and remove the venv | ||
| conda deactivate | ||
| conda remove --name epbd_bert_condavenv_test1 --all -y | ||
| conda remove -p .venvs/epbd_bert_condavenv_test1 --all -y | ||
| Acknowledgements | ||
| ======================================== | ||
| Los Alamos National Lab (LANL), T-1 | ||
|
|
@@ -90,17 +110,23 @@ Authors | |
| - `Anny Usheva <mailto:Anny\_[email protected]>`_: Surgery, Rhode Island Hospital and Brown University | ||
|
|
||
| How to cite EPBD-BERT? | ||
| ================== | ||
| ======================================== | ||
|
|
||
| .. code-block:: console | ||
| @article{kabir2024advancing, | ||
| title = {Advancing Transcription Factor Binding Site Prediction Using DNA Breathing Dynamics and Sequence Transformers via Cross Attention}, | ||
| author = {Kabir, Anowarul and Bhattarai, Manish and Rasmussen, Kim {\O} and Shehu, Amarda and Bishop, Alan R and Alexandrov, Boian and Usheva, Anny}, | ||
| journal = {bioRxiv}, | ||
| pages = {2024--01}, | ||
| year = {2024}, | ||
| publisher = {Cold Spring Harbor Laboratory} | ||
| title = {Advancing Transcription Factor Binding Site Prediction Using DNA Breathing Dynamics and Sequence Transformers via Cross Attention}, | ||
| author = {Kabir, Anowarul and | ||
| Bhattarai, Manish and | ||
| Rasmussen, Kim {\O} and | ||
| Shehu, Amarda and | ||
| Bishop, Alan R and | ||
| Alexandrov, Boian and | ||
| Usheva, Anny}, | ||
| journal = {bioRxiv}, | ||
| pages = {2024--01}, | ||
| year = {2024}, | ||
| publisher= {Cold Spring Harbor Laboratory} | ||
| doi = {10.5281/zenodo.11130474}, | ||
| url = {https://www.biorxiv.org/content/10.1101/2024.01.16.575935v2} | ||
| } | ||
|
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