publications update etc.

docs/people/Babita-Singh.md

@@ -4,6 +4,7 @@ date: 2020-01-16
 person_image_file: "bsingh.jpg"
 person_github_id: babisingh
 person_email: [email protected]
+is_gone: true
 ---
 
 * Structural Variants scout team lead

docs/people/David-Salgado.md

@@ -2,6 +2,7 @@
 title: "David Salgado"															# required
 date: 2020-01-16																		# optional
 person_email: [email protected]							# recommended
+is_gone: true
 ---
 
 * Structural Variants scout team

docs/people/Lauren-Fromont.md

@@ -3,7 +3,7 @@ title: "Lauren Fromont"
 image_file: "lfromont.png"
 description: Project Manager Beacon
 date: 2020-01-01
-is_contact: true
+is_gone: true
 ---
 
 ![](/img/people/lfromont.png){: style="float: right; width: 120px; margin-top: -70px;"}

docs/people/Manuel_Rueda.md

@@ -1,6 +1,7 @@
 ---
 title: "Manuel Rueda"
 date: 2020-01-01
+is_gone: true
 ---
 
 * Developer - Beacon Reference Implementation

docs/people/Rahel-Paloots.md

@@ -2,7 +2,7 @@
 title:  "Rahel Paloots"
 date:   2021-03-15
 image_file: 'rahelp.jpg'
-
+is_gone: true
 ---
 
 * Department of Molecular Life Sciences  

docs/publications/2023-05-17-phenopackets-tools.md

@@ -0,0 +1,16 @@
+---
+title: "Phenopacket-tools: Building and validating GA4GH Phenopackets"
+description: Bioinformatics tools and examples for working with the Phenopackets standard
+template: post.html 
+authors:
+ - '@mbaudis'
+date: 2023-05-17
+pdf_file_name:
+links:
+  - '[article at PLoS ONE](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0285433)'
+  - '[Article PDF](/pdf/2023-05-17___Davis-et-al.__Phenopacket-tools--Building-and-validating-GA4GH-Phenopackets__PLoS-ONE.pdf)'
+---
+
+##### Danis D, Jacobsen JOB, Wagner AH, Groza T, Beckwith MA, Rekerle L, Carmody LC, Reese J, Hegde H, Ladewig MS, Seitz B, Munoz-Torres M, Harris NL, Rambla J, Baudis M, Mungall CJ, Haendel MA, Robinson PN. (2023) **Phenopacket-tools: Building and validating GA4GH Phenopackets.** _PLoS One._ 18:e0285433.
+
+**Abstract** The Global Alliance for Genomics and Health (GA4GH) is a standards-setting organization that is developing a suite of coordinated standards for genomics. The GA4GH Phenopacket Schema is a standard for sharing disease and phenotype information that characterizes an individual person or biosample. The Phenopacket Schema is flexible and can represent clinical data for any kind of human disease including rare disease, complex disease, and cancer. It also allows consortia or databases to apply additional constraints to ensure uniform data collection for specific goals. We present phenopacket-tools, an open-source Java library and command-line application for construction, conversion, and validation of phenopackets. Phenopacket-tools simplifies construction of phenopackets by providing concise builders, programmatic shortcuts, and predefined building blocks (ontology classes) for concepts such as anatomical organs, age of onset, biospecimen type, and clinical modifiers.<!--more--> Phenopacket-tools can be used to validate the syntax and semantics of phenopackets as well as to assess adherence to additional user-defined requirements. The documentation includes examples showing how to use the Java library and the command-line tool to create and validate phenopackets. We demonstrate how to create, convert, and validate phenopackets using the library or the command-line application. Source code, API documentation, comprehensive user guide and a tutorial can be found at https://github.com/phenopackets/phenopacket-tools. The library can be installed from the public Maven Central artifact repository and the application is available as a standalone archive. The phenopacket-tools library helps developers implement and standardize the collection and exchange of phenotypic and other clinical data for use in phenotype-driven genomic diagnostics, translational research, and precision medicine applications.

docs/publications/2024-03-01-Beacon-Tips.md

@@ -0,0 +1,22 @@
+---
+title: "Twelve quick tips for deploying a Beacon"
+description: Some hints for Beacon developers & implementers
+template: post.html 
+authors:
+  - '@mbaudis'
+date: 2024-03-01
+pdf_file_name: 2024-03-01___Fromont-et-al.__Twelve-quick-tips-for-deploying-a-Beacon__PLoS-Comput-Biol.pdf
+links:
+  - '[article at Briefings in PLoS Computational Biology](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011817)'
+---
+
+#### Lauren A Fromont, Mauricio Moldes, Michael Baudis, Anthony J Brookes, Arcadi Navarro and Jordi Rambla
+##### PLoS Comput Biol. 2024 Mar 1;20(3):e1011817.
+* doi: [10.1371/journal.pcbi.1011817](https://doi.org/10.1371/journal.pcbi.1011817).
+* PMID: [38427629](https://pubmed.ncbi.nlm.nih.gov/38427629/)
+
+
+**Introduction**: In the age of data-driven biomedical research and clinical practice, the sharing of genomic and clinical data for health research and personalized medicine has become an important contribu- tor to improved diagnosis and treatment. From the data owner’s perspective, potential benefits include improved treatments, personalization of healthcare practice, and more effective con- trol of disease proliferation. However, the requirement for high levels of data security to pro- tect sensitive information presents a barrier to data discovery and sharing.
+
+Beacon is designed to enable the benefits of data discovery while minimizing the associated risks...
+

docs/publications/2024-03-27-cancercelllines.org.md

@@ -0,0 +1,22 @@
+---
+title: "cancercelllines.org - a Novel Resource for Genomic Variants in Cancer Cell Lines"
+description: DATABASE Article
+template: post.html 
+authors:
+ - '@rahelp'
+ - '@mbaudis'
+date: 2024-03-27
+pdf_file_name: 2024-03-27___Paloots-and-Baudis__cancercelllines.org—a-novel-resource-for-genomic-variants-in-cancer-cell-lines__DATABASE.pdf
+links:
+  - '[Database Article](https://doi.org/10.1093/database/baae030)'
+  - '[preprint at bioarXiv](https://doi.org/10.1101/2023.12.12.571281)'
+---
+
+#### Rahel Paloots and Michael Baudis
+##### Database (Oxford). 2024 Apr 30:2024:baae030.  [doi: 10.1093/database/baae030](https://doi.org/10.1093/database/baae030)
+##### bioarXiv preprint (2023-12-13): [https://doi.org/10.1101/2023.12.12.571281](https://doi.org/10.1101/2023.12.12.571281)
+
+![DATABASE logo](/img/logo-database-journal-300x150.png){: style="float: right; width: 150px; margin-top: -100px;"}
+**Abstract**: Cancer cell lines are an important component in biological and medical research, enabling studies of cellular mechanisms as well as the development and testing of pharmaceuticals. Genomic alterations in cancer cell lines are widely studied as models for oncogenetic events and are represented in a wide range of primary resources. We have created a comprehensive, curated knowledge resource - cancercelllines.org - with the aim to enable easy access to genomic profiling data in cancer cell lines, curated from a variety of resources and integrating both copy number and single nucleotide variants (SNVs) data. We have gathered over 5,600 copy number profiles as well as SNV annotations for 16,000 cell lines and provide this data with mappings to the GRCh38 reference genome. Both genomic variations and associated curated metadata can be queried through the **GA4GH Beacon v2 API** and a graphical user interface with extensive data retrieval enabled using GA4GH data schemas under a permissive licensing scheme.
+
+**Availability and Implementation**: Our resource is publicly available on the web at <https://cancercelllines.org>.

mkdocs.yaml

@@ -2,7 +2,7 @@
 
 nav:
     - Introduction: /
-    - News: news
+    - News & Events: news
     - FAQ: FAQ
     - Publications: publications
     - People: people