{"id":18501590,"url":"https://github.com/const-ae/neural_network_dna_demo","last_synced_at":"2025-04-09T18:33:15.284Z","repository":{"id":82391879,"uuid":"91349380","full_name":"const-ae/Neural_Network_DNA_Demo","owner":"const-ae","description":"Jupyter Notebook to demonstrate the use of Neural Networks for Transcription Factor Binding Site Prediction","archived":false,"fork":false,"pushed_at":"2017-06-20T10:51:38.000Z","size":3366,"stargazers_count":12,"open_issues_count":1,"forks_count":4,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-03-23T20:37:01.842Z","etag":null,"topics":["demo","dna","ipython","neural-network"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/const-ae.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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":"2017-05-15T14:46:40.000Z","updated_at":"2024-12-17T03:58:44.000Z","dependencies_parsed_at":"2023-04-19T23:31:50.656Z","dependency_job_id":null,"html_url":"https://github.com/const-ae/Neural_Network_DNA_Demo","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/const-ae%2FNeural_Network_DNA_Demo","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/const-ae%2FNeural_Network_DNA_Demo/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/const-ae%2FNeural_Network_DNA_Demo/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/const-ae%2FNeural_Network_DNA_Demo/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/const-ae","download_url":"https://codeload.github.com/const-ae/Neural_Network_DNA_Demo/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248087914,"owners_count":21045609,"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":["demo","dna","ipython","neural-network"],"created_at":"2024-11-06T13:54:21.585Z","updated_at":"2025-04-09T18:33:15.244Z","avatar_url":"https://github.com/const-ae.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Neural Network for Sequence Data\n\nThis project is an example how the recent advancements in Neural Networks\ncan be applied to sequence data, namely DNA.\n\nWe will take a collection of sequences plus information if they are \nbound by a transcription factor as input data and after training\na convolutional neural network we will be able to make predictions \nfor new sequences. In addition we will extract what the network learned\nand make a plot of the motif.\n\nThe example are chosen such that it is not necessary to have a GPU and\n should learn just fine on a CPU.\n\n# Preparation\n\nTo make sure everybody can play around with the example easily and you do not need to install the dependencies, please follow the instructions below.\n\nThe code for this tutorial is written in Python and you will need a 2.7 or 3.5 installation (https://www.python.org/downloads/). If you have \n\nNeural Networks are a complex topic and there are quite a few packages you need to install to get going. The easiest way to install packages in Python is to use [Anaconda](https://www.continuum.io/downloads). In the following I will assume that you only have Anaconda installed.\n\n## Libraries\n\nTo run the the code in the tutorial you will need the following libraries:\n\n* Jupyter / IPython\n* Keras\n* Theano _or_ Tensorflow\n* Numpy\n\n## Installation Steps \n\nAfter the successful installation of Anaconda we will create a new conda environment to not pollute the default environment:\n\n```Shell\n$ conda create -n seqnn python=3.5 \n```\n\n```Shell\n# On Windows\n$ activate seqnn\n# On Mac / Linux\n$ source activate seqnn\n```\n\nInstall Theano\n\n```Shell\n$ conda install theano pygpu\n```\n\nInstall other dependencies\n\n```Shell\n$ conda install scikit-learn keras numpy scipy matplotlib ipython jupyter pandas sympy nose nb_conda\n```\n\nDownload the `Neural_Network_DNA_Demo` project either by cloning it with git\n\n```Shell\n$ git clone https://github.com/const-ae/Neural_Network_DNA_Demo.git\n```\n\n__OR__ download this [zip file](https://github.com/Artjom-Metro/Neural_Network_DNA_Demo/archive/master.zip) and extracting it somewhere.\n\nMove with the command line to the `Neural_Network_DNA_Demo` folder:\n\n```Shell\n$ cd \u003cLOCATION_OF_DOWNLOAD\u003e/Neural_Network_DNA_Demo\n```\n\nand start the Jupyter notebook:\n\n```Shell\n$ jupyter notebook\n```\n\nA new browser page should open where you can click on the `.ipynb` file\nand start experimenting.\n\n\n# Problems, Issues etc.\n\nIf you have problems with the installation of ...\n\n* ... Theano --\u003e check [this](http://deeplearning.net/software/theano/install.html#install) guide\n* ... Keras --\u003e check [this](https://keras.io/#installation) guide\n\nor just open an issue [here](https://github.com/const-ae/Neural_Network_DNA_Demo/issues).\n\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fconst-ae%2Fneural_network_dna_demo","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fconst-ae%2Fneural_network_dna_demo","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fconst-ae%2Fneural_network_dna_demo/lists"}