{"id":14514,"date":"2025-01-06T20:36:13","date_gmt":"2025-01-07T01:36:13","guid":{"rendered":"https:\/\/ptp.cloud\/?p=14514"},"modified":"2025-09-15T21:32:53","modified_gmt":"2025-09-16T01:32:53","slug":"alphafold-optimization-healthomics-ptp","status":"publish","type":"post","link":"https:\/\/ptp.cloud\/alphafold-optimization-healthomics-ptp\/","title":{"rendered":"How PTP Enabled 12x Faster AlphaFold Workflows and 86% Cost Savings with AWS HealthOmics"},"content":{"rendered":"[et_pb_section fb_built=”1″ custom_padding_last_edited=”on|tablet” admin_label=”Section” _builder_version=”4.27.4″ _module_preset=”default” background_color=”#3e489d” background_image=”https:\/\/ptp.cloud\/wp-content\/uploads\/2024\/10\/Square-Pattern-Hero-Background.png” custom_padding=”5px||||false|false” custom_padding_tablet=”40px||40px||true|false” custom_padding_phone=”40px||40px||true|false” da_disable_devices=”off|off|off” locked=”off” global_colors_info=”{}” da_is_popup=”off” da_exit_intent=”off” da_has_close=”on” da_alt_close=”off” da_dark_close=”off” da_not_modal=”on” da_is_singular=”off” da_with_loader=”off” da_has_shadow=”on”][et_pb_row column_structure=”2_3,1_3″ make_equal=”on” _builder_version=”4.27.4″ _module_preset=”default” width=”85%” max_width=”1380px” custom_padding=”63px||1px|||” global_colors_info=”{}”][et_pb_column type=”2_3″ module_class=”col-vert-cent” _builder_version=”4.27.4″ _module_preset=”default” global_colors_info=”{}”][et_pb_heading title=”How PTP Enabled 12x Faster AlphaFold Workflows and 86% Cost Savings* with AWS HealthOmics” _builder_version=”4.27.4″ _module_preset=”default” title_font=”–et_global_heading_font|700|||||||” title_text_color=”#ffffff” title_font_size=”3.5rem” title_line_height=”1.2em” max_width_tablet=”620px” max_width_phone=”620px” max_width_last_edited=”on|tablet” custom_padding=”40px||||false|false” global_colors_info=”{}”][\/et_pb_heading][\/et_pb_column][et_pb_column type=”1_3″ module_class=”col-vert-cent” _builder_version=”4.27.4″ _module_preset=”default” global_colors_info=”{}”][et_pb_image src=”https:\/\/ptp.cloud\/wp-content\/uploads\/2024\/10\/PTP-Hero-Section-Goat-Illustration-min.png” alt=”Illustration of Goat working on servers leading data to the cloud and to a proved treatment” title_text=”PTP Hero Section Goat Illustration” align=”center” disabled_on=”on|off|off” _builder_version=”4.27.4″ _module_preset=”default” max_width_tablet=”75%” max_width_phone=”75%” max_width_last_edited=”on|tablet” custom_padding=”25px||25px||true|false” global_colors_info=”{}”][\/et_pb_image][\/et_pb_column][\/et_pb_row][et_pb_row make_equal=”on” _builder_version=”4.27.4″ _module_preset=”default” width=”85%” max_width=”1380px” custom_margin=”|auto|29px|auto||” global_colors_info=”{}”][et_pb_column type=”4_4″ module_class=”col-vert-cent” _builder_version=”4.27.4″ _module_preset=”default” global_colors_info=”{}”][et_pb_text _builder_version=”4.27.4″ _module_preset=”default” text_font=”–et_global_heading_font|300|||||||” text_text_color=”#ffffff” text_font_size=”1.5rem” text_line_height=”2.1rem” max_width_tablet=”620px” max_width_phone=”620px” max_width_last_edited=”on|tablet” global_colors_info=”{}”]\n

A biotechnology firm in stealth mode, dedicated to advancing vaccines for global health, leveraged AlphaFold to predict and understand protein structures using machine learning. AlphaFold, powered by convolutional neural networks (CNN), offers groundbreaking insights but requires extensive computational resources. Before engaging PTP, the company faced severe limitations with their on-premises infrastructure, hindering their ability to scale AlphaFold effectively.<\/span><\/p>\n[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row column_structure=”1_2,1_2″ _builder_version=”4.27.4″ _module_preset=”default” global_colors_info=”{}”][et_pb_column type=”1_2″ _builder_version=”4.27.4″ _module_preset=”default” global_colors_info=”{}”][et_pb_number_counter title=”*The HealthOmics deployment resulted in an 86% cost reduction compared to the initial proof of concept deployment using AWS.” number=”86″ _builder_version=”4.27.4″ _module_preset=”default” title_text_color=”#ffffff” global_colors_info=”{}”][\/et_pb_number_counter][\/et_pb_column][et_pb_column type=”1_2″ _builder_version=”4.27.4″ _module_preset=”default” global_colors_info=”{}”][et_pb_number_counter title=”Freed from static on-prem constraints, the company\u2019s workflows accelerated by 12 times.” number=”12x” percent_sign=”off” _builder_version=”4.27.4″ _module_preset=”default” title_text_color=”#ffffff” global_colors_info=”{}”][\/et_pb_number_counter][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ admin_label=”section” _builder_version=”4.16″ custom_padding=”32px||1px|||” da_disable_devices=”off|off|off” locked=”off” global_colors_info=”{}” da_is_popup=”off” da_exit_intent=”off” da_has_close=”on” da_alt_close=”off” da_dark_close=”off” da_not_modal=”on” da_is_singular=”off” da_with_loader=”off” da_has_shadow=”on”][et_pb_row column_structure=”1_2,1_2″ make_equal=”on” _builder_version=”4.27.4″ _module_preset=”default” width=”85%” max_width=”1380px” custom_padding=”8px||1px|||” global_colors_info=”{}”][et_pb_column type=”1_2″ _builder_version=”4.27.4″ _module_preset=”default” global_colors_info=”{}”][et_pb_text _builder_version=”4.27.4″ _module_preset=”default” text_font=”–et_global_heading_font||||||||” text_text_color=”gcid-secondary-color” text_font_size=”28px” text_line_height=”2rem” custom_margin=”45px||||false|false” custom_padding=”||||false|false” text_font_size_tablet=”28px” text_font_size_phone=”24px” text_font_size_last_edited=”on|phone” global_colors_info=”{%22gcid-secondary-color%22:%91%22text_text_color%22%93}”]\n

The Challenge<\/strong><\/span><\/h2>\n[\/et_pb_text][\/et_pb_column][et_pb_column type=”1_2″ _builder_version=”4.27.4″ _module_preset=”default” global_colors_info=”{}”][\/et_pb_column][\/et_pb_row][et_pb_row make_equal=”on” _builder_version=”4.27.4″ _module_preset=”default” width=”85%” max_width=”1380px” custom_padding=”2px||63px|||” locked=”off” global_colors_info=”{}”][et_pb_column type=”4_4″ module_class=”col-vert-cent” _builder_version=”4.27.4″ _module_preset=”default” global_colors_info=”{}”][et_pb_text _builder_version=”4.27.4″ _module_preset=”default” text_font=”–et_global_heading_font|300|||||||” text_text_color=”gcid-secondary-color” text_font_size=”28px” text_line_height=”2.3rem” custom_margin=”||7px|||” text_font_size_tablet=”28px” text_font_size_phone=”24px” text_font_size_last_edited=”on|phone” global_colors_info=”{%22gcid-secondary-color%22:%91%22text_text_color%22,%22text_text_color%22,%22text_text_color%22%93}”]\n

The company\u2019s existing infrastructure presented several roadblocks:<\/span><\/p>\n

Limited GPU Access
<\/strong>AlphaFold was deployed on individual laptops or a single server with restricted GPU capabilities. Their laptops lacked GPU provisioning, and the server\u2019s GPU capacity was physically constrained.<\/span><\/p>\n

Insufficient Storage
<\/strong>The server lacked adequate storage to process lab data simultaneously, creating significant bottlenecks.<\/span><\/p>\n

On-Prem Environment
<\/strong>The company\u2019s reliance on on-premises infrastructure severely limited scalability, and they had no prior experience using AWS<\/a>.<\/span><\/p>\n

Unpredictable Workload Scaling
<\/strong>The complexity of AlphaFold\u2019s computational requirements made predicting resource needs difficult, rendering additional on-prem purchases financially unviable.<\/span><\/p>\n

Lack of Cloud Expertise
<\/strong>The team lacked the technical expertise to implement and scale AlphaFold workflows in the cloud.<\/span><\/p>\n

To progress toward their research targets, the company needed a scalable solution to run AlphaFold efficiently, reduce costs, and accelerate processing times.<\/span><\/p>\n[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ custom_padding_last_edited=”on|tablet” next_background_color=”#ffffff” admin_label=”Section” _builder_version=”4.27.4″ _module_preset=”default” background_color=”#3e489d” background_image=”https:\/\/ptp.cloud\/wp-content\/uploads\/2024\/10\/Square-Pattern-Hero-Background.png” custom_padding=”||52px||false|false” custom_padding_tablet=”40px||40px||true|false” custom_padding_phone=”40px||40px||true|false” bottom_divider_style=”arrow” bottom_divider_height=”83px” da_disable_devices=”off|off|off” locked=”off” global_colors_info=”{}” da_is_popup=”off” da_exit_intent=”off” da_has_close=”on” da_alt_close=”off” da_dark_close=”off” da_not_modal=”on” da_is_singular=”off” da_with_loader=”off” da_has_shadow=”on”][et_pb_row make_equal=”on” _builder_version=”4.27.4″ _module_preset=”default” width=”85%” max_width=”1380px” custom_padding=”||99px|||” global_colors_info=”{}”][et_pb_column type=”4_4″ module_class=”col-vert-cent” _builder_version=”4.27.4″ _module_preset=”default” global_colors_info=”{}”][et_pb_text _builder_version=”4.27.4″ _module_preset=”default” text_font=”–et_global_heading_font||||||||” text_text_color=”gcid-secondary-color” text_font_size=”28px” text_line_height=”2rem” custom_margin=”||0px||false|false” custom_padding=”||16px|||” text_font_size_tablet=”28px” text_font_size_phone=”24px” text_font_size_last_edited=”on|phone” global_colors_info=”{%22gcid-secondary-color%22:%91%22text_text_color%22%93}”]\n

The Solution<\/strong><\/span>\u00a0<\/h2>\n[\/et_pb_text][et_pb_text _builder_version=”4.27.4″ _module_preset=”default” text_font=”–et_global_heading_font|300|||||||” text_text_color=”#ffffff” text_font_size=”28px” text_line_height=”2.3rem” custom_margin=”||0px|||” text_font_size_tablet=”28px” text_font_size_phone=”24px” text_font_size_last_edited=”on|phone” global_colors_info=”{}”]\n

PTP introduced a cloud-scale computing platform to address the company\u2019s challenges and accelerate their research goals:<\/p>\n

Initial Proof of Concept<\/strong>
PTP migrated the company\u2019s data to Amazon S3<\/a> and deployed AlphaFold on traditional EC2<\/a> compute resources to demonstrate cloud viability.<\/p>\n

This proof of concept validated that AWS could match or exceed their on-prem performance.<\/p>\n

Optimized Deployment<\/strong>
PTP evaluated two deployment options for AlphaFold: AWS Batch<\/strong><\/a> for a bespoke deployment and AWS HealthOmics<\/strong><\/a>.<\/p>\n

The company selected HealthOmics due to its advanced security features, robust storage capabilities, and native integration with NextFlow<\/a> for managing workflows.<\/p>\n

Custom HealthOmics Deployment<\/strong>
HealthOmics supported the deployment of AlphaFold\u2019s \u201cReady to Run\u201d version but required customization for the company\u2019s complex project, which involved processing more than 12,000 residues (compared to the standard 1,200).<\/p>\n

PTP adjusted existing scripting and deployment code within HealthOmics, enabling faster development and scalability.<\/p>\n

Scalable Infrastructure<\/strong>
PTP\u2019s deployment provided the company with access to multiple servers and GPUs, drastically reducing computational times from days to hours.<\/p>\n[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ admin_label=”section” _builder_version=”4.16″ custom_padding=”32px||1px|||” da_disable_devices=”off|off|off” locked=”off” global_colors_info=”{}” da_is_popup=”off” da_exit_intent=”off” da_has_close=”on” da_alt_close=”off” da_dark_close=”off” da_not_modal=”on” da_is_singular=”off” da_with_loader=”off” da_has_shadow=”on”][et_pb_row make_equal=”on” _builder_version=”4.27.4″ _module_preset=”default” width=”85%” max_width=”1380px” custom_margin=”54px|auto||auto||” custom_padding=”2px||0px|||” global_colors_info=”{}”][et_pb_column type=”4_4″ _builder_version=”4.27.4″ _module_preset=”default” global_colors_info=”{}”][et_pb_text _builder_version=”4.27.4″ _module_preset=”default” text_font=”–et_global_heading_font||||||||” text_text_color=”gcid-secondary-color” text_font_size=”28px” text_line_height=”2rem” custom_margin=”||3px|||” custom_padding=”||38px|||” text_font_size_tablet=”28px” text_font_size_phone=”24px” text_font_size_last_edited=”on|phone” global_colors_info=”{%22gcid-secondary-color%22:%91%22text_text_color%22%93}”]\n

Infrastructure Diagram<\/strong><\/span><\/h2>\n[\/et_pb_text][et_pb_text _builder_version=”4.27.4″ _module_preset=”default” text_font=”–et_global_heading_font|300|||||||” text_text_color=”rgba(0,0,0,0.66)” text_font_size=”20px” text_line_height=”2.3rem” custom_padding=”||40px|||” text_font_size_tablet=”28px” text_font_size_phone=”24px” text_font_size_last_edited=”on|phone” global_colors_info=”{}”]\n

\"AWS<\/p>\n

Figure 1: Reference Architecture for Proof-of-Concept Deployment for The company<\/span><\/i><\/p>\n

\"AWS<\/i><\/p>\n

Figure 2: Reference Architecture for Custom HealthOmics Deployment\u00a0<\/span><\/i><\/p>\n[\/et_pb_text][et_pb_divider _builder_version=”4.27.4″ _module_preset=”default” global_colors_info=”{}”][\/et_pb_divider][\/et_pb_column][\/et_pb_row][et_pb_row make_equal=”on” _builder_version=”4.27.4″ _module_preset=”default” width=”85%” max_width=”1380px” custom_margin=”36px|auto||auto||” custom_padding=”2px||81px|||” global_colors_info=”{}”][et_pb_column type=”4_4″ _builder_version=”4.27.4″ _module_preset=”default” global_colors_info=”{}”][et_pb_text _builder_version=”4.27.4″ _module_preset=”default” text_font=”–et_global_heading_font|300|||||||” text_text_color=”rgba(0,0,0,0.78)” text_font_size=”28px” text_line_height=”2rem” custom_margin=”||3px|||” custom_padding=”||11px|||” text_font_size_tablet=”28px” text_font_size_phone=”24px” text_font_size_last_edited=”on|phone” global_colors_info=”{}”]\n

The Outcome<\/strong><\/span><\/h2>\n


<\/strong><\/span>PTP\u2019s engagement delivered transformative results:<\/span><\/p>\n

<\/strong><\/span><\/p>\n[\/et_pb_text][et_pb_text _builder_version=”4.27.4″ _module_preset=”default” text_font=”–et_global_heading_font|300|||||||” text_text_color=”rgba(0,0,0,0.66)” text_font_size=”28px” text_line_height=”2.3rem” custom_padding=”25px|25px|25px|25px|true|true” text_font_size_tablet=”28px” text_font_size_phone=”24px” text_font_size_last_edited=”on|phone” border_radii=”on|2px|2px|2px|2px” border_width_all=”1px” global_colors_info=”{}”]\n

12x Faster Workflows<\/strong>
Freed from static on-prem constraints, the company\u2019s workflows accelerated by 12 times<\/strong>.<\/span><\/p>\n

86% Cost Savings<\/strong>
The HealthOmics deployment resulted in an 86% cost reduction<\/span><\/strong> compared to the initial proof of concept deployment using AWS.<\/p>\n

Massive Cost Avoidance<\/strong>
Transitioning from on-prem infrastructure eliminated the need for significant equipment purchases, maintenance costs, and man-hours.<\/p>\n

Improved Scalability<\/strong>
The custom HealthOmics deployment allowed the company to scale AlphaFold workflows efficiently and process highly complex data sets.<\/p>\n[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row column_structure=”1_2,1_2″ module_class=”vert-cent” _builder_version=”4.27.4″ _module_preset=”default” width=”85%” max_width=”1380px” custom_margin=”0px||0px||false|false” custom_padding=”0px||0px||false|false” locked=”off” global_colors_info=”{}”][et_pb_column type=”1_2″ module_id=”contact” _builder_version=”4.27.4″ _module_preset=”default” global_colors_info=”{}”][et_pb_image src=”https:\/\/ptp.cloud\/wp-content\/uploads\/2024\/12\/Graphs-Isometric-Contained-Icon.png” alt=”Graphs Isometric Contained Icon” title_text=”Graphs Isometric Contained Icon” show_bottom_space=”off” disabled_on=”on|off|off” _builder_version=”4.27.4″ _module_preset=”default” width_tablet=”200px” width_phone=”150px” width_last_edited=”on|phone” custom_margin=”|||-20px|false|false” global_colors_info=”{}”][\/et_pb_image][et_pb_heading title=”Ready to scale your computational workflows? ” _builder_version=”4.27.4″ _module_preset=”default” title_level=”h2″ title_font=”–et_global_heading_font|600|||||||” title_text_align=”left” title_text_color=”gcid-0e52a8f4-5dfd-4102-9f40-fd354ef9edd5″ title_font_size=”2.88rem” title_line_height=”1.2em” max_width_tablet=”100%” max_width_phone=”300px” max_width_last_edited=”on|phone” custom_margin=”15px||5px||false|false” locked=”off” global_colors_info=”{%22gcid-0e52a8f4-5dfd-4102-9f40-fd354ef9edd5%22:%91%22title_text_color%22%93}”][\/et_pb_heading][et_pb_text _builder_version=”4.27.4″ _module_preset=”default” text_font=”Ubuntu||||||||” text_text_color=”#000000″ text_font_size=”1.25rem” text_line_height=”1.75rem” max_width=”620px” locked=”off” global_colors_info=”{}”]\n

By leveraging PTP\u2019s cloud expertise and AWS HealthOmics, the company significantly reduced costs, accelerated research timelines, and optimized functionality. <\/span>Contact PTP today to learn how we can help optimize your cloud environment for research and innovation.<\/span><\/p>\n

 <\/p>\n[\/et_pb_text][et_pb_button button_url=”https:\/\/outlook.office365.com\/owa\/calendar\/PTP1@pinnacletechpartners.com\/bookings\/” url_new_window=”on” button_text=”Schedule a call” button_alignment=”left” _builder_version=”4.27.4″ _module_preset=”default” custom_button=”on” button_text_size=”18px” button_text_color=”#ffffff” button_bg_color=”gcid-primary-color” button_border_width=”0px” button_border_radius=”50px” button_font=”Ubuntu|500|||||||” button_use_icon=”off” custom_padding=”0.8rem|1.8rem|0.8rem|1.8rem|true|true” button_text_size_tablet=”1rem” button_text_size_phone=”1rem” button_text_size_last_edited=”on|tablet” locked=”off” global_colors_info=”{%22gcid-primary-color%22:%91%22button_bg_color%22%93,%22gcid-4a2771a4-2bac-479e-b2cf-583957402471%22:%91%22button_bg_color__hover%22%93}” button_bg_color__hover=”#0c71c3″ button_bg_color__hover_enabled=”on|desktop”][\/et_pb_button][\/et_pb_column][et_pb_column type=”1_2″ _builder_version=”4.27.4″ _module_preset=”default” background_color=”#2f348d” custom_padding=”60px|60px|25px|60px|false|true” custom_padding_tablet=”60px|60px|25px|60px|false|true” custom_padding_phone=”30px|30px|0px|30px|false|true” custom_padding_last_edited=”on|tablet” border_radii=”on|10px|10px|10px|10px” global_colors_info=”{}”][et_pb_text _builder_version=”4.27.4″ _module_preset=”default” text_font=”Ubuntu||||||||” text_text_color=”#FFFFFF” text_font_size=”18px” text_line_height=”1.4em” header_2_font=”Ubuntu|500|||||||” header_2_text_color=”#FFFFFF” header_2_font_size=”38px” header_2_line_height=”1.2em” global_colors_info=”{}”]\n

Let us help you unlock your potential.<\/strong><\/h2>\n

Contact PTP today to learn how we can deliver cost-efficient, scalable, and compliant cloud solutions for your business.<\/p>\n[\/et_pb_text][et_pb_code _builder_version=”4.27.4″ _module_preset=”default” hover_enabled=”0″ global_colors_info=”{}” sticky_enabled=”0″]

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