Merge branch 'main' into wilco

greenelab · Apr 11, 2024 · 7651d96 · 7651d96
2 parents f1a2094 + 4c3d369
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diff --git a/_data/tools.yaml b/_data/tools.yaml
@@ -1,9 +1,9 @@
-- name: Gplas
+- name: gplas2
   group: wgs
-  image: images/gplas_logo.png
-  link: https://gitlab.com/mmb-umcu/gplas
+  image: images/gplas2_logo.png
+  link: https://gitlab.com/mmb-umcu/gplas2
   description: gplas is a tool to bin plasmid-predicted contigs based on sequence composition, coverage and assembly graph information. This tool extends the possibility of accurately binning predicted plasmid contigs into several discrete plasmid components.
-  repo: mmb-umcu/gplas
+  repo: mmb-umcu/gplas2
   tags: 
     - Plasmid
 
@@ -49,7 +49,15 @@
   repo: mmb-umcu/plasmidec
   tags:
     - Plasmid
-
+
+- name: plasmidCC
+  group: wgs
+  image: images/plasmidCC_tmp_logo.png
+  link: https://gitlab.com/mmb-umcu/plasmidCC
+  description: "plasmidCC is a plasmid classification tool that uses Centrifuge to predict the origin of contigs (plasmid or chromosome). Out of the box, plasmidCC can be used to predict plasmid contigs of a selected number of species. By supplying a custom Centrifuge database, plasmidCC can be used for any desired species."
+  repo: mmb-umcu/plasmidCC
+  tags:
+    - Plasmid
 
 - name: Bactofidia
   group: wgs

diff --git a/_members/anita-schurch.md b/_members/anita-schurch.md
@@ -1,7 +1,7 @@
 ---
 name: Anita Schurch
 image: images/people/anita-schurch.jpg
-description: Assistant Professor
+description: Associate Professor
 status: current
 role: pi
 aliases:

diff --git a/_members/bart-boogaard.md b/_members/bart-boogaard.md
@@ -0,0 +1,17 @@
+---
+name: Bart Boogaard
+image: images/people/bart-boogaard.jpg
+description: Student
+role: student
+status: current
+aliases:
+  - B. P. Boogaard
+  - Bart P. Boogaard
+links: 
+  email: b.p.boogaard-3@umcutrecht.nl
+  gitlab: bboogaa3
+  github: bboogaard-3
+  linkedin: bart-boogaard-1125591b2/
+---
+
+I'm Bart, a former MSc Drug Innovation student with a newly found interest in programming. Following my 6 month internship in which I worked on a project about analysis and visualization of metagenomic data, I remained at the MMB-BioIT group to continue developing an R package for these purposes. 
diff --git a/_members/janetta-top.md b/_members/janetta-top.md
@@ -9,7 +9,11 @@ aliases:
 
 links:
   email: J.Top@umcutrecht.nl
-  orcid: 
-  github: 
+  orcid: 0000-0002-4620-8128
+  github: janettatop
   linkedin: 
 ---
+
+I’m assistant professor in the group of Rob Willems at the Medical Microbiology Department at the UMCU.
+
+I am coordinating the microbiome facility, which includes the contact with medical departments within the UMCU that collect samples from chorts of patients, supervision of technicians in the lab who perform the wet-lab part, including DNA extractions and sequencing and I also perform the downstream analysis of the data. We mainly perform 16S rRNA analysis and metagenomics shotgun sequencing. For the analysis, I make use of the bioinformatic pipelines developed within the BioIT group and R-scripts. 
diff --git a/_members/oscar-jordan.md b/_members/oscar-jordan.md
@@ -0,0 +1,22 @@
+---
+name: Oscar Jordan
+image: images/people/oscar-jordan.jpg
+description: Student
+status: current
+role: student
+aliases:
+  - Oscar Jordan
+  - O Jordan
+  - O. Jordan
+links:
+  home-page:
+  email: o.jordan@students.uu.nl
+  orcid:
+  github: oscarjordan5
+  gitlab: oscarjordan
+  linkedin: oscar-jordan-ba867724b
+---
+
+I’m a master student from Utrecht University, currently working at the UMC for the Medical Microbiology Department.
+
+I’m working on a bioinformatics tool to reconstruct plasmids from fragmented short read assembly graphs.
diff --git a/images/Group_picture_2024.jpeg b/images/Group_picture_2024.jpeg
diff --git a/images/gplas2_logo.png b/images/gplas2_logo.png
diff --git a/images/people/bart-boogaard.jpg b/images/people/bart-boogaard.jpg
diff --git a/images/people/bart-boogaard_party.jpg b/images/people/bart-boogaard_party.jpg
diff --git a/images/plasmidCC_tmp_logo.png b/images/plasmidCC_tmp_logo.png
diff --git a/index.md b/index.md
@@ -10,7 +10,7 @@ The Medical Microbiology bioinformatics (MMB-BioIT) team from the University Med
 {% include section.html full=true %}
 
 {% include figure.html
-  image="images/UMCU-1.jpg"
+  image="images/Group_picture_2024.jpg"
 %}
 
 {% include section.html %}

diff --git a/team/index.md b/team/index.md
@@ -95,9 +95,9 @@ nav:
 
 ## Join
 
-We have no open positions at the moment.
+Internship positions will be advertised on KonJoin 
 
-{% include link.html type="external" link="https://google.com/" text="Apply Now" icon="" style="button" %}
+{% include link.html type="external" link="https://uu.konjoin.nl/profile/anita-schurch/" text="KonJoin" icon="" style="button" %}
 {:.center}
 
 {% include section.html %}