change readme.md

README.md

 
-# 1. 从GitHub下载安装CIRI-deep环境
+
+
+# 论文
+CIRI-Deep Enables Single-Cell and Spatial Transcriptomic Analysis of Circular RNAs with Deep Learning
+https://onlinelibrary.wiley.com/doi/10.1002/advs.202308115
+
+
+
+# 模型结构
+CIRI-deep模型可有效用于各转录组样本间推断差异剪接环形RNA，拓展了环形RNA的研究范围，为环形RNA研究提供了新的高效分析方法。同时，CIRI-deepA模型可以提供单细胞及空间水平环形RNA的有效解析，
+
+![img](./images/image.png)
+
+
+
+# 算法原理
+CIRI deep通过深度神经网络对circRNA的顺式特征和样本对（总RNA或富含poly（A）的RNA）的RBP表达进行训练。
+
+![Alt text](./images/image-1.png)
+
+
+# 环境配置
+## Docker（方法一）
+
+```
+docker pull image.sourcefind.cn:5000/dcu/admin/base/pytorch:2.1.0-ubuntu20.04-dtk24.04.1-py3.10
+docker run -dit --shm-size 80g --network=host --name=CIRI --privileged --device=/dev/kfd --device=/dev/dri --group-add video --cap-add=SYS_PTRACE --security-opt seccomp=unconfined -u root -v /opt/hyhal/:/opt/hyhal/:ro image.sourcefind.cn:5000/dcu/admin/base/pytorch:2.1.0-ubuntu20.04-dtk24.04.1-py3.10    /bin/bash
+docker exec -it CIRI /bin/bash
 ```
-git clone https://github.com/gyjames/CIRIdeep.git
+
+安装依赖
+
+```
+pip install ./whl/tensorflow-1.15.1+git06e2e8aa.dtk2404-cp37-cp37m-linux_x86_64.whl
+pip install -r requirements.txt  -i http://mirrors.aliyun.com/pypi/simple/ --trusted-host mirrors.aliyun.com
+```
+
+
+
+## Dockerfile（方法二）
 
 ```
-# 安装环境
-
-```
-conda create -n  CIRIdeep  python=3.7
-source activate CIRIdeep
-pip install tensorflow-1.15.1+git06e2e8aa.dtk2404-cp37-cp37m-linux_x86_64.whl
-pip install -r requirements.txt
-pip install 'h5py<3.0.0' 
-pip install protobuf==3.20.1  -i https://pypi.tuna.tsinghua.edu.cn/simple 
-
-```
-
-环境安装包如下：
-```
-absl-py              2.1.0
-astor                0.8.1
-certifi              2022.12.7
-cycler               0.11.0
-gast                 0.2.2
-google-pasta         0.2.0
-grpcio               1.62.3
-h5py                 2.10.0
-importlib-metadata   6.7.0
-joblib               1.3.2
-Keras                2.3.1
-Keras-Applications   1.0.8
-Keras-Preprocessing  1.1.2
-kiwisolver           1.4.5
-Markdown             3.4.4
-MarkupSafe           2.1.5
-matplotlib           3.3.4
-numpy                1.19.2
-opt-einsum           3.3.0
-pandas               1.1.5
-Pillow               9.5.0
-pip                  22.3.1
-protobuf             3.20.1
-pyparsing            3.1.2
-python-dateutil      2.9.0.post0
-pytz                 2024.1
-PyYAML               6.0.1
-scikit-learn         0.24.2
-scipy                1.7.3
-setuptools           65.6.3
-six                  1.16.0
-tensorboard          1.15.0
-tensorflow           1.15.1+git06e2e8aa.dtk2404
-tensorflow-estimator 1.15.1
-termcolor            2.3.0
-threadpoolctl        3.1.0
-typing_extensions    4.7.1
-Werkzeug             2.2.3
-wheel                0.38.4
-wrapt                1.16.0
-zipp                 3.15.0
-```
-
-
-
-# 测试
+docker build -t geneformer:latest .
+docker run -dit --shm-size 80g --network=host --name=geneformer --privileged --device=/dev/kfd --device=/dev/dri --group-add video --cap-add=SYS_PTRACE --security-opt seccomp=unconfined -u root -v /opt/hyhal/:/opt/hyhal/:ro geneformer:latest /bin/bash
+docker exec -it CIRI /bin/bash
+```
+
+## anaconda
+
+1.创建conda虚拟环境：
+
+```
+conda create -n  CIRI  python=3.7
+conda activate CIRI 
+```
+
+2.其它依赖库参照requirements.txt安装：
+
+```
+pip install ./whl/tensorflow-1.15.1+git06e2e8aa.dtk2404-cp37-cp37m-linux_x86_64.whl
+pip install -r requirements.txt -i http://mirrors.aliyun.com/pypi/simple/ --trusted-host mirrors.aliyun.com
+```
+
+
+# 预测
+
 
 ## 用CIRI-deep进行预测
 ```
 python CIRIdeep.py predict -geneExp_absmax ./demo/RBPmax_totalRNA.tsv -seqFeature ./demo/cisfeature.tsv -splicing_max ./demo/splicingamount_max.tsv -predict_list ./demo/predict_list.txt -model_path ./models/CIRIdeep.h5 -outdir ./outdir -RBP_dir ./demo/RBPexp_total -splicing_dir ./demo/splicingamount
 
 ```
+
+输出文件在outputdir下
+
+![Alt text](./images/image3.png)
+
+
+
 ## 用CIRI-deepA进行预测
 
 ```
 python CIRIdeep.py predict -geneExp_absmax ./demo/RBPmax_polyA.tsv -seqFeature ./demo/cisfeature.tsv -predict_list ./demo/predict_list.txt -model_path ./models/CIRIdeepA.h5 -outdir ./outdir -RBP_dir ./demo/RBPexp_polyA --CIRIdeepA
 ```
 
+输出文件在outputdir下
+
+![Alt text](./images/image4.png)
+
+
 
 
-# 参考文档
+# 应用场景
 
 
+## 算法类别
+ai for science
+
+## 行业 
+科研
+
+##  医疗  
+科研  高校
+
+
+# 源码仓库及问题反馈
+
+```
+git@developer.sourcefind.cn:modelzoo/cirideep.git
+```
+
+# 参考资料
 
 ```
-https://github.com/gyjames/CIRIdeep.git
+git clone https://github.com/gyjames/CIRIdeep.git
 ```
+
+
+
+
+

dockerfile

+FROM image.sourcefind.cn:5000/dcu/admin/base/pytorch:2.1.0-ubuntu20.04-dtk24.04.1-py3.10
+RUN source /opt/dtk-24.04.1/env.sh
+RUN cp /usr/share/zoneinfo/Asia/Shanghai /etc/localtime && echo 'Asia/Shanghai' >/etc/timezone 
+ENV LANG C.UTF-8

requirements.txt

@@ -3,4 +3,6 @@ matplotlib==3.3.4
 numpy==1.19.2
 pandas==1.1.5
 scikit-learn==0.24.2
+protobuf==3.20.1 
+h5py<3.0.0
 #python