Refactoring for Portal linking

config.toml

@@ -32,29 +32,40 @@ twitter = "BioComputeObj"
 identifier = "home"
 name = "Documentation Home"
 url = "/"
-
 weight = 1
 
+[[menu.primary]]
+identifier = "about"
+name = "About "
+url = "/about"
+weight = 2
+
 [[menu.primary]]
 identifier = "user_guide"
 name = "User Guide"
 url = "/user_guide"
-weight = 2
+weight = 3
 
 [[menu.primary]]
 identifier = "best_practices"
 name = "Best Practices"
 url = "/best_practices"
-weight = 3
+weight = 4
 
 [[menu.primary]]
 identifier = "sop"
-name = "BioCompute Curation SOP"
+name = "Curation SOP"
 url = "/sop"
-weight = 4
+weight = 5
+
+[[menu.primary]]
+identifier = "events"
+name = "News & Events"
+url = "/events"
+weight = 6
 
 [[menu.primary]]
 identifier = "biocomputeobject.org"
-name = "BioCompute Object Home"
-url = "https://www.biocomputeobject.org/"
-weight = 5
+name = "BioCompute Portal"
+url = "http://portal.biochemistry.gwu.edu/"
+weight = 7

content/about.md

@@ -0,0 +1,73 @@
+---
+title: "About"
+menu: "main"
+---
+
+<div class="col-lg-6 offset-lg-3 text-center">
+<img src="/images/logo.about.png" class="img-fluid mx-auto d-block" width="75%" alt="BioCompute Logo">
+</div>
+
+<br>
+
+### What is BioCompute?
+
+Tremendous insights can be found in genome data, and many of these insights are being used to drive personalized medicine. But the hundreds of millions of reads that come from a gene sequencer represent small, nearly random fragments of the genome that's being sequenced, and there are countless ways in which that data can be transformed to yield insights into cancer, ancestry, microbiome dynamics, metagenomics, and many other areas of interest.
+
+Because there are so many different platforms and so many different scripts and tools to analyze genome data, there is a great need to standardize the way in which these steps are communicated. The more analysis steps and the more complicated a pipeline, the greater the need for a standardized mechanism of communication. The BioCompute standard brings clarity to an analysis, making it clear and reproducible.
+
+<div class="col-lg-10 offset-lg-1 text-center">
+<img src="/images/about.3.png" class="img-fluid mx-auto d-block" alt="">
+</div>
+
+<br>
+
+A BioCompute Object (BCO) is an instance of the BioCompute standard, and is a computational record of a bioinformatics pipeline. A BCO is not an analysis, but is a record of which analyses were executed and in exactly which ways. In this way, a BCO acts as an interface for existing standards. A BCO contains all of the necessary information to repeat an entire pipeline from FASTQ to result, and includes additional metadata to identify provenance and usage.
+
+### WiFi Analogy
+
+The [802.11 standard](https://en.wikipedia.org/wiki/IEEE_802.11) (more commonly called "WiFi") is a way of standardizing communication between vastly different products on a wireless network. If a product manufacturer wants a product to be able to communicate on a wireless internet network, they can configure the device to use the WiFi standard and it will be able to communicate with most commercial routers, regardless of whether the product is a Mac, a PC, a cell phone, or a smart toaster.
+
+<div class="col-lg-8 offset-lg-2 text-center">
+<img src="/images/about.4.png" class="img-fluid mx-auto d-block" alt="">
+</div>
+
+<br>
+
+BioCompute fills a similar need. BioCompute is not an automation or a new programming language, it is a way of collecting and communicating information between two entities. Rather than a latop and a router, it may be between a pharmaceutical company and the FDA, or between two clinicians, or between a clinician and a researcher. In much the same way that WiFi does not standardize the data that's being transmitted -- allowing you to use Apple's Facetime, Microsoft's Internet Explorer, or your favorite cell phone app -- BioCompute does not standardize the platforms or tools that are used for genome analysis. You continue to use your favorite platforms and tools, whether it's [HIVE](https://hive.biochemistry.gwu.edu/dna.cgi?cmd=main), [Galaxy](https://galaxyproject.org/), [Seven Bridges](https://www.sevenbridges.com/), [DNAnexus](https://www.dnanexus.com/), or others. Also like WiFi, BioCompute can be layered with other privacy or security protocols depending on usage. So clinical trial data can be secured and HIPAA-compliant, while government-funded data sets shared between researchers can be completely open access.
+
+Because BioCompute acts like an envelope for an entire analysis pipeline, it is compatible with other existing standards, including [FHIR Genomics](https://www.hl7.org/fhir/genomics.html) and [GA4GH](https://www.ga4gh.org/).
+
+### BioCompute Description
+
+BioCompute is written in [Javascript Object Notation (JSON)](https://json.org/example.html), which is simply a set of key:value pairs (meaning that raw files can be read without any knowledge of programming). Information within the BCO is organized into "domains." The domains within a BCO record are Provenance, Usability, Extension, Description, Execution, Input/Output, and Parametric Domains. For more information on the domains, please see the [BioCompute Schema](https://gitlab.com/IEEE-SA/2791/ieee-2791-schema).
+
+BioCompute was built through a collaboration between The George Washington University and the FDA to improve communication of bioinformatics pipelines, and has since been expanded and refined through the participation or collaboration of hundreds of participants from throughout the public and private sectors. While we welcome interest and membership from anyone, most users will fall into one of three categories:
+
+- [Research Community](/research) <br>
+  The Biocompute standard can help substantially improve replicability, making it possible to repeat a pipeline on a different sample with high fidelity and high confidence.
+
+- [Clinical Community](/clinical) <br>
+  As BioCompute Objects become tested and validated, they can be applied in the clinic to identify risk factors, flag pharmakogenetic information, and much more.
+
+- [Pharma, Biotech and Regulatory Pipeline](/regulatory) <br>
+  Protracted communications with the FDA can extend the review process by months. A standardized method of communicating HTS data may help repeat results more quickly and without the need for additional communication.
+
+Research, clinical, and regulatory groups are key drivers of personalized medicine that is based on next generation sequencing, but there are barriers between these groups. BioCompute reduces these hurdles and brings transparency to the workflow, making it more clear what was done, and clearly delineating expectations for data sharing. The BioCompute specification can be layered with other privacy and security protocols to guard sensitive data, or be made open source depending on the needs of the user.
+
+The BioCompute project has generated two publications, three workshops, FDA funding, contributions from over 300 participants, and FDA submissions. The project has worked with individuals from NIH, Harvard, several biotech and pharma companies, EMBL-EBI, Galaxy Project, and many more, and can be integrated with any existing standard for HTS data. The project is expected to be both an IEEE and ISO recognized standard within 8-10 months.
+
+More information about The current BioCompute standard can be found on the [Open Science Foundation website](https://osf.io/h59uh/) (where the standard is developed and maintained), the [HIVE](https://hive.biochemistry.gwu.edu/htscsrs/biocompute) website, and the [Research Objects discussion of BioCompute](http://www.researchobject.org/2017-11-27-biocompute-objects/).
+
+<div class="col-lg-12 text-center">
+<img src="/images/about.2.png" class="img-fluid mx-auto d-block" alt="">
+</div>
+
+<br>
+
+<div class="alert alert-primary" role="alert">
+
+**Milestones in the BioCompute Program**
+
+The major milestones of the BioCompute Partnership and future goals are paving the way for a consensus-driven, widely adopted standard. The FDA's Genomics Working Group (GWG) originally articulated the challenges of communicating genomic analysis pipelines in a regulatory context in 2013. Since then, the project has accumulated tremendous momentum, a testament to the GWG's efforts in describing communication challenges. More recently, the second BioCompute publication has recently been published, the 4th Workshop is scheduled, and the next major goal is the formal launch of the BioCompute Public Private Partnership. The [Executive Committee](https://www.biocomputeobject.org/leadership.html) will formalize the future roadmap beyond these goals.
+
+</div>

content/events.md

@@ -0,0 +1,140 @@
+---
+title: "Events"
+menu: "main"
+---
+
+<div class="col-lg-8 offset-lg-2 text-center">
+<img src="/images/logo.workshop.png" class="img-fluid mx-auto d-block" alt="">
+</div>
+
+<br>
+
+Welcome! This is the BioCompute Events page. Workshops are listed on the schedule below. For any questions, comments, or for a BioCompute Informational Session (15 minute WebEx) click [here](/contact)
+
+<br>
+
+
+<div class="row" >
+
+<div class="col-lg-9" markdown="1">
+
+<h2>Previous Workshops</h2>
+<h3>2021</h3>
+<h3><a name="7-28-21"></a>Towards Interoperability: Generating BioCompute Objects on Cloud-Based Platforms for Advancing Precision Medicine</h3>
+<h3><a href="https://www.eventbrite.com/e/workflow-capture-reproducibility-biocompute-objects-in-seven-bridges-p-tickets-162673277151">Register here! </a></h3>
+
+<b>Date</b>: Wednesday July 28 at 11:00AM-12:30PM ET
+
+<b>Purpose</b>: The purpose of this workshop is to understand the value of interoperability in both research and regulatory review for scientists in the public or private spaces, and especially from the perspective of FDA personnel. As part of the larger goal of smoothing communication between the FDA and private sector to reduce organization burden on both ends, this workshop will first introduce how the cloud computing platform Seven Bridges can package BioCompute Objects (BCOs) for workflow capture and reproducibility. Following the introduction, we will describe several  previously observed use cases to solicit feedback on their relevance to attendees, potentially from image processing (for diagnosis), machine-learning (for communicating and exchanging models with training data), and/or multi-modal data applications. Agenda can be found on the registration page.
+
+<b>Speaker</b>: Dr. Dennis A. Dean, II is a Principal Investigator at Seven Bridges. He manages and builds interdisciplinary teams that develop complex tools and conduct data analyses from conception to deployment/completion. He leads the Translational Science and Analytics Team that includes data scientists, bioinformaticians, and genomic data scientists. He is responsible for the success of his team members across commercial, government, and internal projects. He leads collaborations with the U.S. Food and Drug Administration (FDA), the U.S. Department of Veteran Affairs Million Veteran Program (MVP) and collaborates with large pharmaceutical companies. Dr. Dean trained as a research fellow in medicine at the Harvard Medical School and Brigham and Women’s Hospital in the Program for Sleep Epidemiology and the Program for Sleep and Cardiovascular Medicine. He earned his Ph.D. in biomedical engineering and biotechnology and M.S. in computer science from the University of Massachusetts. He earned his B.S. in computer science from SUNY, Empire State College.
+
+<br>
+
+<h4><a name="5-12-21"></a>Workflow Preservation and Reproducibility with BCO-RO</h4>
+
+<b>Date</b>: Wednesday May 12 at 11:00AM-12:30PM ET
+
+
+<b>Purpose</b>: Training session showing how Research Objects (RO) can package BioCompute Objects (BCO) for Digital Preservation and Reproducibility. Research Objects (RO) are a machine-readable digital preservation effort that aims to package all constituent elements of an analysis together into one archive with very detailed provenance. Here, Stian Soiland-Reyes, a Technical Architect on the Research Objects project, will describe an example that packages the workflow as a descriptive, human-readable report in the form of a BioCompute Object (BCO), and which bundles everything in an RO "Crate." Stian will explain the Research Objects project, and introduce a tutorial for building an RO-BCO archive. RO-BCOs can be efficient solutions for scaling up data analyses, both for internal record keeping and logistics, and for communicating workflows to outside groups.
+
+
+<h3>2020</h3>
+
+<h4><a name="11-20-20"></a>Introduction to workflow portability with BCO-CWL</h4>
+
+<b>Date</b>: Friday November 20th at 12-2PM ET
+
+
+<b>Purpose</b>: BioCompute Objects (BCOs) were developed to aid in communicating a more thorough understanding of computational analyses. While BCOs can be leveraged for re-execution within the context of specific platforms that have integrated them, they are not used for cross platform implementations. Common Workflow Language (CWL) was developed to assist in the portability of execution, meaning the ability to reproduce a pipeline in a different computational environment. The BCO and CWL teams have partnered over the last year to develop a joint mechanism that enables both portability of execution and strong human- and machine-readable documentation through metadata records. New functionality of BCO-CWL means that a reviewer may be able to independently run a computational pipeline used by a sponsor if using a command line environment, or on a platform that supports CWL. This presentation will go over the project by introducing the concept of portability of execution, the concept of a CWL file, and demonstrate the initial draft of a BCO-CWL implementation.
+<br>
+<br>
+<h4><a name="03-18-20"></a>BioCompute Advisory Boards Workshop</h4>
+
+<b>Date</b>: Wednesday March 18, 2020 2-4pm ET
+
+<b>Purpose</b>: The purpose of this workshop is to facilitate dialogue between Advisory Board(s) members on BioCompute applications, vocabulary, and current + future progression of the project through a hands-on approach. These discussions are a means to obtain feedback, introduce potential use-cases, and bring everyone up to speed about BioCompute.
+<br>
+<br>
+<h4><a name="06-24-20"></a>BioCompute Workshop for Reviewers: Tool for Communicating Sequencing Analysis</h4>
+
+<b>Date</b>: Wednesday June 24, 2020 10am-12pm ET
+
+<b>Purpose</b>: The purpose of this workshop is to facilitate dialogue and show BCO utility specifically for FDA reviewers. We will be briefly discussing BioCompute applications, vocabulary, current + future progression of the project in addition to a hands-on approach to reviewing a BCO for. These discussions are a means to introduce BCO as a tool for submission evaluation mechanism obtain feedback.
+
+<ul>
+	<li><i>Slide deck available [here](/docs/ReviewerWorkshop_24June2020_Deck.pdf)</i></li>
+	<li><i>Quick reference guide can be found [here](/docs/BCOCheatSheet.pdf) (PDF)</i></li>
+	<li><i>Post-workshop attendee survey available [here](https://www.surveymonkey.com/r/Q9LXSC6)</i></li>
+</ul>
+<br>
+
+<h4><a name="09-24-20"></a>BioCompute Objects: Methods for communicating provenance of data and analysis</h4>
+
+<h6><i>Part of the <a href="https://www.biocuration.org/biocuration-2020-online-workshops/">Biocuration 2020 Online Workshop</a> series</i></h6>
+
+<b>Date</b>: Thursday September 24, 9am PT, 12pm ET, 5pm CET
+
+<b>Organizers</b>: Charles Hadley King, Raja Mazumder, Jonathon Keeney; George Washington University
+
+<b>Purpose</b>: Inform about BioCompute Object use and purpose and offer tutelage in the creation and use of BCOs
+
+<ul><li>Abstract available <a href="https://drive.google.com/file/d/1aYdfM6Ph2eJ9a1-1s96vFyiFQGkCtmsY/view">here</a></li></ul>
+
+<br>
+
+<h2>2019<h2>
+
+<h4><a name="05-14-19"></a>BioCompute Objects: Tools for Communicating NGS Data and Analysis</h4>
+
+<b>Date</b>: Tuesday May 14, 2019
+
+<b>Organizers</b>: [FDA Center for Biologics Evaluation and Research (CBER)](https://www.fda.gov/about-fda/fda-organization/center-biologics-evaluation-and-research-cber)
+
+**Purpose:** The BioCompute project has resulted in three prior workshops, two publications, several collaborations, and is currently undergoing formal balloting to become an official IEEE standard. The upcoming Workshop will engage more stakeholders in creating and using BioCompute for NGS and other bioinformatics data analysis communications with the FDA. Specifically, the Workshop will have two components: use case examples, and hands on & demonstrations of new tools that leverage BioCompute. A new Precision FDA-BioCompute Challenge will also be launched at the event.
+
+<ul>
+
+<li>Agenda <a href="/2019-workshop-agenda">here</a></li>
+<li>Meeting info <a href="https://www.fda.gov/vaccines-blood-biologics/workshops-meetings-conferences-biologics/biocompute-objects-tools-communicating-ngs-data-and-analysis-public-workshop-05142019-05152019">here</a></li>
+
+</ul>
+
+<br>
+
+<h2>2018</h2>
+
+<h4><a name="05-14-19"></a>BioCompute Objects PoC Workshop</h4>
+<ul>
+<li>Agenda <a href="https://hive.biochemistry.gwu.edu/htscsrs/agenda_2018">here</a></li>
+</ul>
+
+<br>
+
+<h2>2014</h2>
+
+<h4><a name="09-24-2014">2014 Public Workshop: Next Generation Sequencing Standards</h4>
+
+<ul>
+<li>
+<a href="http://wayback.archive-it.org/7993/20180125145708/https://www.fda.gov/ScienceResearch/SpecialTopics/RegulatoryScience/ucm389561.htm)">Agenda and meeting info</a>
+</li>
+</ul>
+
+</div>
+
+<div class="col-lg-3">
+
+<a class="twitter-timeline" 
+  href="https://twitter.com/BioComputeObj?ref_src=twsrc%5Etfw" 
+    data-height="2500"
+    show-replies="true"
+    data-chrome="nofooter"
+    data-chrome="noheader"
+    dnt="true">
+  Tweets by BioComputeObj</a> 
+  <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
+
+</div>
+
+<br>

content/extension-scm.md

@@ -1,5 +1,5 @@
 ---
-title: "BCO Introduction"
+title: "Extension to External References: Software Configuration Management (SCM)"
 menu: "main"
 ---