Simulation Workflows and Batch Processing

A processing workflow is part of connecting AnyBody simulations with external data and delivering selected output to subsequent processes (analysis, reporting, etc.). A processing workflow hides the simulation and makes it fully or partially automated.

The objective is to integrate frequently done simulations as part of your daily work, or to enable processing (and re-processing) of large datasets that requires similar simulations, e.g., for multiple trials for many subjects/patients, minimize the risk of errors during execution of simulations, increase the ease of use for running the workflow using simple configuration settings.

Processing workflow with AnyBody can be customized with many processing tools. AnyBody Technology recommends and deliver custom solutions typically using the following processing tools.

AnyPyTools

AnyPyTools is a toolkit for working with the AnyBody Modeling System (AMS) from Python. Its main purpose is to organize, run and collect output from simulations. It has a scheduler to launch multiple instances of AMS utilizing computers with multiple cores. AnyPyTools makes it easy to do parameter and sensitivity analyses and many other things which is not possible directly within AMS. This can be used to streamline the process of running multiple simulations while still being able to change settings for each simulation directly from Python.

Visualization and user interaction

To combine the workflow into an easy-to-use product we build custom frontend solutions using the Python based framework Dash Python library. Whether you need a specific dashboard to inspect data results, plot relevant analysis result or create reports, we can help you achieve this. Our product can be operated locally as a desktop application or ported to the cloud for easy sharing between teams, organizations, or users.

SnakeMake workflow management system

To orchestrate workflows involving multiple steps and large amounts of data we utilize the Python based SnakeMake project. Key features include the option to scale into server, grid, cluster, and cloud environments, set hardware requirements, human readable code, modularization for reusable workflow blocks and much more.

Cloud Hosting

To help you getting started without having to manage servers, workflows, and separate applications, we provide an end-to-end cloud hosting of a simulation workflow. We take care of setting up servers, hosting, AnyBody models, processing, data extractions, and presentation into graphs and reports – all accessible from your browser.

Top
[contact-form-7 id="5120" title="Contact Form optin monster"]
<div class="wpcf7 no-js" id="wpcf7-f5120-o1" lang="da-DK" dir="ltr"> <div class="screen-reader-response"><p role="status" aria-live="polite" aria-atomic="true"></p> <ul></ul></div> <form action="/services/simulation-workflows-and-batch-processing/#wpcf7-f5120-o1" method="post" class="wpcf7-form init" aria-label="Kontaktformular" novalidate="novalidate" data-status="init"> <div style="display: none;"> <input type="hidden" name="_wpcf7" value="5120" /> <input type="hidden" name="_wpcf7_version" value="5.7.2" /> <input type="hidden" name="_wpcf7_locale" value="da_DK" /> <input type="hidden" name="_wpcf7_unit_tag" value="wpcf7-f5120-o1" /> <input type="hidden" name="_wpcf7_container_post" value="0" /> <input type="hidden" name="_wpcf7_posted_data_hash" value="" /> <input type="hidden" name="_wpcf7_recaptcha_response" value="" /> </div> <div class="wrapper" style="overflow:hidden; vertical-align:middle; height:50px;"> <div class="div1" style="float:left; width:45%; margin-right:10px; font-size:14px;"> <p><span class="wpcf7-form-control-wrap" data-name="First-name"><input size="40" class="wpcf7-form-control wpcf7-text wpcf7-validates-as-required" aria-required="true" aria-invalid="false" placeholder="First name" value="" type="text" name="First-name" /></span> </p> </div> <div class="div2" style="float:left; width:45%; font-size:14px;"> <p><span class="wpcf7-form-control-wrap" data-name="Last-name"><input size="40" class="wpcf7-form-control wpcf7-text wpcf7-validates-as-required" aria-required="true" aria-invalid="false" placeholder="Last name" value="" type="text" name="Last-name" /></span> </p> </div> </div> <div class="wrapper" style="overflow:hidden; vertical-align:middle; height:50px;"> <div class="div1" style="float:left; width:45%; margin-right:10px; font-size:14px;"> <p><span class="wpcf7-form-control-wrap" data-name="E-mail"><input size="40" class="wpcf7-form-control wpcf7-text wpcf7-email wpcf7-validates-as-required wpcf7-validates-as-email" aria-required="true" aria-invalid="false" placeholder="E-mail" value="" type="email" name="E-mail" /></span> </p> </div> <div class="div2" style="float:left; width:45%; font-size:14px;"> <p><span class="wpcf7-form-control-wrap" data-name="Job-title"><input size="40" class="wpcf7-form-control wpcf7-text wpcf7-validates-as-required" aria-required="true" aria-invalid="false" placeholder="Job title" value="" type="text" name="Job-title" /></span> </p> </div> </div> <div class="wrapper" style="overflow:hidden; vertical-align:middle; font-size:14px; height:50px;"> <div class="div1" style="float:left; width:45%; margin-right:10px; font-size:14px;"> <p><span class="wpcf7-form-control-wrap" data-name="Organization"><input size="40" class="wpcf7-form-control wpcf7-text wpcf7-validates-as-required" aria-required="true" aria-invalid="false" value="Organization name" type="text" name="Organization" /></span> </p> </div> <div class="div1" style="float:left; width:45%; margin-right:10px; font-size:14px;"> <p><span class="wpcf7-form-control-wrap" data-name="Organization-website"><input size="40" class="wpcf7-form-control wpcf7-text wpcf7-validates-as-required" aria-required="true" aria-invalid="false" placeholder="Organization website" value="" type="text" name="Organization-website" /></span> </p> </div> </div> <div class="wrapper" style="overflow:hidden; vertical-align:middle; font-size:14px; height:50px;"> <div class="div1" style="float:left; width:45%; margin-right:10px; font-size:14px;"> <p><span class="wpcf7-form-control-wrap country_auto country_auto-623"><select class="wpcf7-form-control wpcf7-select country_auto wpcf7-country_auto" aria-invalid="false" name="country_auto-623" ><option value="0" data-id="0" >Select Country</option><option value='Afghanistan' data-id='1'>Afghanistan</option><option value='Aland Islands' data-id='2'>Aland Islands</option><option value='Albania' data-id='3'>Albania</option><option value='Algeria' data-id='4'>Algeria</option><option value='American Samoa' data-id='5'>American Samoa</option><option value='Andorra' data-id='6'>Andorra</option><option value='Angola' data-id='7'>Angola</option><option value='Anguilla' data-id='8'>Anguilla</option><option value='Antarctica' data-id='9'>Antarctica</option><option value='Antigua And Barbuda' data-id='10'>Antigua And Barbuda</option><option value='Argentina' data-id='11'>Argentina</option><option value='Armenia' data-id='12'>Armenia</option><option value='Aruba' data-id='13'>Aruba</option><option value='Australia' data-id='14'>Australia</option><option value='Austria' data-id='15'>Austria</option><option value='Azerbaijan' data-id='16'>Azerbaijan</option><option value='Bahamas The' data-id='17'>Bahamas The</option><option value='Bahrain' data-id='18'>Bahrain</option><option value='Bangladesh' data-id='19'>Bangladesh</option><option value='Barbados' data-id='20'>Barbados</option><option value='Belarus' data-id='21'>Belarus</option><option value='Belgium' data-id='22'>Belgium</option><option value='Belize' data-id='23'>Belize</option><option value='Benin' data-id='24'>Benin</option><option value='Bermuda' data-id='25'>Bermuda</option><option value='Bhutan' data-id='26'>Bhutan</option><option value='Bolivia' data-id='27'>Bolivia</option><option value='Bosnia and Herzegovina' data-id='28'>Bosnia and Herzegovina</option><option value='Botswana' data-id='29'>Botswana</option><option value='Bouvet Island' data-id='30'>Bouvet Island</option><option value='Brazil' data-id='31'>Brazil</option><option value='British Indian Ocean Territory' data-id='32'>British Indian Ocean Territory</option><option value='Brunei' data-id='33'>Brunei</option><option value='Bulgaria' data-id='34'>Bulgaria</option><option value='Burkina Faso' data-id='35'>Burkina Faso</option><option value='Burundi' data-id='36'>Burundi</option><option value='Cambodia' data-id='37'>Cambodia</option><option value='Cameroon' data-id='38'>Cameroon</option><option value='Canada' data-id='39'>Canada</option><option value='Cape Verde' data-id='40'>Cape Verde</option><option value='Cayman Islands' data-id='41'>Cayman Islands</option><option value='Central African Republic' data-id='42'>Central African Republic</option><option value='Chad' data-id='43'>Chad</option><option value='Chile' data-id='44'>Chile</option><option value='China' data-id='45'>China</option><option value='Christmas Island' data-id='46'>Christmas Island</option><option value='Cocos (Keeling) Islands' data-id='47'>Cocos (Keeling) Islands</option><option value='Colombia' data-id='48'>Colombia</option><option value='Comoros' data-id='49'>Comoros</option><option value='Congo' data-id='50'>Congo</option><option value='Congo The Democratic Republic Of The' data-id='51'>Congo The Democratic Republic Of The</option><option value='Cook Islands' data-id='52'>Cook Islands</option><option value='Costa Rica' data-id='53'>Costa Rica</option><option value='Cote D&#039;Ivoire (Ivory Coast)' data-id='54'>Cote D&#039;Ivoire (Ivory Coast)</option><option value='Croatia (Hrvatska)' data-id='55'>Croatia (Hrvatska)</option><option value='Cuba' data-id='56'>Cuba</option><option value='Cyprus' data-id='57'>Cyprus</option><option value='Czech Republic' data-id='58'>Czech Republic</option><option value='Denmark' data-id='59'>Denmark</option><option value='Djibouti' data-id='60'>Djibouti</option><option value='Dominica' data-id='61'>Dominica</option><option value='Dominican Republic' data-id='62'>Dominican Republic</option><option value='East Timor' data-id='63'>East Timor</option><option value='Ecuador' data-id='64'>Ecuador</option><option value='Egypt' data-id='65'>Egypt</option><option value='El Salvador' data-id='66'>El Salvador</option><option value='Equatorial Guinea' data-id='67'>Equatorial Guinea</option><option value='Eritrea' data-id='68'>Eritrea</option><option value='Estonia' data-id='69'>Estonia</option><option value='Ethiopia' data-id='70'>Ethiopia</option><option value='Falkland Islands' data-id='71'>Falkland Islands</option><option value='Faroe Islands' data-id='72'>Faroe Islands</option><option value='Fiji Islands' data-id='73'>Fiji Islands</option><option value='Finland' data-id='74'>Finland</option><option value='France' data-id='75'>France</option><option value='French Guiana' data-id='76'>French Guiana</option><option value='French Polynesia' data-id='77'>French Polynesia</option><option value='French Southern Territories' data-id='78'>French Southern Territories</option><option value='Gabon' data-id='79'>Gabon</option><option value='Gambia The' data-id='80'>Gambia The</option><option value='Georgia' data-id='81'>Georgia</option><option value='Germany' data-id='82'>Germany</option><option value='Ghana' data-id='83'>Ghana</option><option value='Gibraltar' data-id='84'>Gibraltar</option><option value='Greece' data-id='85'>Greece</option><option value='Greenland' data-id='86'>Greenland</option><option value='Grenada' data-id='87'>Grenada</option><option value='Guadeloupe' data-id='88'>Guadeloupe</option><option value='Guam' data-id='89'>Guam</option><option value='Guatemala' data-id='90'>Guatemala</option><option value='Guernsey and Alderney' data-id='91'>Guernsey and Alderney</option><option value='Guinea' data-id='92'>Guinea</option><option value='Guinea-Bissau' data-id='93'>Guinea-Bissau</option><option value='Guyana' data-id='94'>Guyana</option><option value='Haiti' data-id='95'>Haiti</option><option value='Heard and McDonald Islands' data-id='96'>Heard and McDonald Islands</option><option value='Honduras' data-id='97'>Honduras</option><option value='Hong Kong S.A.R.' data-id='98'>Hong Kong S.A.R.</option><option value='Hungary' data-id='99'>Hungary</option><option value='Iceland' data-id='100'>Iceland</option><option value='India' data-id='101'>India</option><option value='Indonesia' data-id='102'>Indonesia</option><option value='Iran' data-id='103'>Iran</option><option value='Iraq' data-id='104'>Iraq</option><option value='Ireland' data-id='105'>Ireland</option><option value='Israel' data-id='106'>Israel</option><option value='Italy' data-id='107'>Italy</option><option value='Jamaica' data-id='108'>Jamaica</option><option value='Japan' data-id='109'>Japan</option><option value='Jersey' data-id='110'>Jersey</option><option value='Jordan' data-id='111'>Jordan</option><option value='Kazakhstan' data-id='112'>Kazakhstan</option><option value='Kenya' data-id='113'>Kenya</option><option value='Kiribati' data-id='114'>Kiribati</option><option value='Korea North' data-id='115'>Korea North</option><option value='Korea South' data-id='116'>Korea South</option><option value='Kuwait' data-id='117'>Kuwait</option><option value='Kyrgyzstan' data-id='118'>Kyrgyzstan</option><option value='Laos' data-id='119'>Laos</option><option value='Latvia' data-id='120'>Latvia</option><option value='Lebanon' data-id='121'>Lebanon</option><option value='Lesotho' data-id='122'>Lesotho</option><option value='Liberia' data-id='123'>Liberia</option><option value='Libya' data-id='124'>Libya</option><option value='Liechtenstein' data-id='125'>Liechtenstein</option><option value='Lithuania' data-id='126'>Lithuania</option><option value='Luxembourg' data-id='127'>Luxembourg</option><option value='Macau S.A.R.' data-id='128'>Macau S.A.R.</option><option value='Macedonia' data-id='129'>Macedonia</option><option value='Madagascar' data-id='130'>Madagascar</option><option value='Malawi' data-id='131'>Malawi</option><option value='Malaysia' data-id='132'>Malaysia</option><option value='Maldives' data-id='133'>Maldives</option><option value='Mali' data-id='134'>Mali</option><option value='Malta' data-id='135'>Malta</option><option value='Man (Isle of)' data-id='136'>Man (Isle of)</option><option value='Marshall Islands' data-id='137'>Marshall Islands</option><option value='Martinique' data-id='138'>Martinique</option><option value='Mauritania' data-id='139'>Mauritania</option><option value='Mauritius' data-id='140'>Mauritius</option><option value='Mayotte' data-id='141'>Mayotte</option><option value='Mexico' data-id='142'>Mexico</option><option value='Micronesia' data-id='143'>Micronesia</option><option value='Moldova' data-id='144'>Moldova</option><option value='Monaco' data-id='145'>Monaco</option><option value='Mongolia' data-id='146'>Mongolia</option><option value='Montenegro' data-id='147'>Montenegro</option><option value='Montserrat' data-id='148'>Montserrat</option><option value='Morocco' data-id='149'>Morocco</option><option value='Mozambique' data-id='150'>Mozambique</option><option value='Myanmar' data-id='151'>Myanmar</option><option value='Namibia' data-id='152'>Namibia</option><option value='Nauru' data-id='153'>Nauru</option><option value='Nepal' data-id='154'>Nepal</option><option value='Netherlands Antilles' data-id='155'>Netherlands Antilles</option><option value='Netherlands The' data-id='156'>Netherlands The</option><option value='New Caledonia' data-id='157'>New Caledonia</option><option value='New Zealand' data-id='158'>New Zealand</option><option value='Nicaragua' data-id='159'>Nicaragua</option><option value='Niger' data-id='160'>Niger</option><option value='Nigeria' data-id='161'>Nigeria</option><option value='Niue' data-id='162'>Niue</option><option value='Norfolk Island' data-id='163'>Norfolk Island</option><option value='Northern Mariana Islands' data-id='164'>Northern Mariana Islands</option><option value='Norway' data-id='165'>Norway</option><option value='Oman' data-id='166'>Oman</option><option value='Pakistan' data-id='167'>Pakistan</option><option value='Palau' data-id='168'>Palau</option><option value='Palestinian Territory Occupied' data-id='169'>Palestinian Territory Occupied</option><option value='Panama' data-id='170'>Panama</option><option value='Papua new Guinea' data-id='171'>Papua new Guinea</option><option value='Paraguay' data-id='172'>Paraguay</option><option value='Peru' data-id='173'>Peru</option><option value='Philippines' data-id='174'>Philippines</option><option value='Pitcairn Island' data-id='175'>Pitcairn Island</option><option value='Poland' data-id='176'>Poland</option><option value='Portugal' data-id='177'>Portugal</option><option value='Puerto Rico' data-id='178'>Puerto Rico</option><option value='Qatar' data-id='179'>Qatar</option><option value='Reunion' data-id='180'>Reunion</option><option value='Romania' data-id='181'>Romania</option><option value='Russia' data-id='182'>Russia</option><option value='Rwanda' data-id='183'>Rwanda</option><option value='Saint Helena' data-id='184'>Saint Helena</option><option value='Saint Kitts And Nevis' data-id='185'>Saint Kitts And Nevis</option><option value='Saint Lucia' data-id='186'>Saint Lucia</option><option value='Saint Pierre and Miquelon' data-id='187'>Saint Pierre and Miquelon</option><option value='Saint Vincent And The Grenadines' data-id='188'>Saint Vincent And The Grenadines</option><option value='Saint-Barthelemy' data-id='189'>Saint-Barthelemy</option><option value='Saint-Martin (French part)' data-id='190'>Saint-Martin (French part)</option><option value='Samoa' data-id='191'>Samoa</option><option value='San Marino' data-id='192'>San Marino</option><option value='Sao Tome and Principe' data-id='193'>Sao Tome and Principe</option><option value='Saudi Arabia' data-id='194'>Saudi Arabia</option><option value='Senegal' data-id='195'>Senegal</option><option value='Serbia' data-id='196'>Serbia</option><option value='Seychelles' data-id='197'>Seychelles</option><option value='Sierra Leone' data-id='198'>Sierra Leone</option><option value='Singapore' data-id='199'>Singapore</option><option value='Slovakia' data-id='200'>Slovakia</option><option value='Slovenia' data-id='201'>Slovenia</option><option value='Solomon Islands' data-id='202'>Solomon Islands</option><option value='Somalia' data-id='203'>Somalia</option><option value='South Africa' data-id='204'>South Africa</option><option value='South Georgia' data-id='205'>South Georgia</option><option value='South Sudan' data-id='206'>South Sudan</option><option value='Spain' data-id='207'>Spain</option><option value='Sri Lanka' data-id='208'>Sri Lanka</option><option value='Sudan' data-id='209'>Sudan</option><option value='Suriname' data-id='210'>Suriname</option><option value='Svalbard And Jan Mayen Islands' data-id='211'>Svalbard And Jan Mayen Islands</option><option value='Swaziland' data-id='212'>Swaziland</option><option value='Sweden' data-id='213'>Sweden</option><option value='Switzerland' data-id='214'>Switzerland</option><option value='Syria' data-id='215'>Syria</option><option value='Taiwan' data-id='216'>Taiwan</option><option value='Tajikistan' data-id='217'>Tajikistan</option><option value='Tanzania' data-id='218'>Tanzania</option><option value='Thailand' data-id='219'>Thailand</option><option value='Togo' data-id='220'>Togo</option><option value='Tokelau' data-id='221'>Tokelau</option><option value='Tonga' data-id='222'>Tonga</option><option value='Trinidad And Tobago' data-id='223'>Trinidad And Tobago</option><option value='Tunisia' data-id='224'>Tunisia</option><option value='Turkey' data-id='225'>Turkey</option><option value='Turkmenistan' data-id='226'>Turkmenistan</option><option value='Turks And Caicos Islands' data-id='227'>Turks And Caicos Islands</option><option value='Tuvalu' data-id='228'>Tuvalu</option><option value='Uganda' data-id='229'>Uganda</option><option value='Ukraine' data-id='230'>Ukraine</option><option value='United Arab Emirates' data-id='231'>United Arab Emirates</option><option value='United Kingdom' data-id='232'>United Kingdom</option><option value='United States' data-id='233'>United States</option><option value='United States Minor Outlying Islands' data-id='234'>United States Minor Outlying Islands</option><option value='Uruguay' data-id='235'>Uruguay</option><option value='Uzbekistan' data-id='236'>Uzbekistan</option><option value='Vanuatu' data-id='237'>Vanuatu</option><option value='Vatican City State (Holy See)' data-id='238'>Vatican City State (Holy See)</option><option value='Venezuela' data-id='239'>Venezuela</option><option value='Vietnam' data-id='240'>Vietnam</option><option value='Virgin Islands (British)' data-id='241'>Virgin Islands (British)</option><option value='Virgin Islands (US)' data-id='242'>Virgin Islands (US)</option><option value='Wallis And Futuna Islands' data-id='243'>Wallis And Futuna Islands</option><option value='Western Sahara' data-id='244'>Western Sahara</option><option value='Yemen' data-id='245'>Yemen</option><option value='Zambia' data-id='246'>Zambia</option><option value='Zimbabwe' data-id='247'>Zimbabwe</option></select></span> </p> </div> </div> <div class="div1" style="width:97%; font-size:14px;"> <p><span class="wpcf7-form-control-wrap" data-name="your-message"><textarea cols="40" rows="10" class="wpcf7-form-control wpcf7-textarea" aria-invalid="false" placeholder="Reason for inquiry" name="your-message"></textarea></span> </p> </div> <div class="div1" style="font-size:12px; margin:5px 5px;"> <p><span class="wpcf7-form-control-wrap" data-name="checkbox-543"><span class="wpcf7-form-control wpcf7-checkbox wpcf7-validates-as-required"><span class="wpcf7-list-item first"><label><span class="wpcf7-list-item-label">Send me price information</span><input type="checkbox" name="checkbox-543[]" value="Send me price information" tabindex="" /></label></span><span class="wpcf7-list-item last"><label><span class="wpcf7-list-item-label">Send me a trial license</span><input type="checkbox" name="checkbox-543[]" value="Send me a trial license" tabindex="" /></label></span></span></span> </p> </div> <p style="font-size:11px; margin-top:5px; margin-bottom: 5px;">By submitting this form, you consent to receive email communications about the AnyBody Modeling System. You can unsubscribe at any time. </p> <p><input class="wpcf7-form-control has-spinner wpcf7-submit" type="submit" value="Send" /> </p><div class="wpcf7-response-output" aria-hidden="true"></div></form></div>