Merge branch 'issue-26' into 'master'

Major update: Automatic generation of index and harmonisation

See merge request !117

.ci/generateIndex.py

+from asyncore import loop
+import os, re
+from os import path
+from pathlib import Path
+from datetime import datetime
+
+def line_prepender(filename, line):
+    with open(filename, 'r+') as f:
+        content = f.read()
+        f.seek(0, 0)
+        f.write(line.rstrip('\r\n') + '\n' + content)
+
+def build_link(title, href):
+
+    # add relative url
+    href = "{{ '" + href + "' | relative_url }}"
+
+    title = title.replace('"', ' ').rstrip().lstrip()
+
+    return f'\t<li><a href="{href}">{title}</a></li>\n'
+
+def save_tag(localroot, root, filename, tag):
+    return_tag = ""
+    os.chdir(root)
+
+    length_tag = len(tag)
+
+    with open(filename, 'r') as f:
+        for line in f:
+            # check for the start of the section
+            if line[0:length_tag+1] == tag + ":":
+                return_tag = line[length_tag+2:]
+                break
+
+    # change back to the local root
+    os.chdir(localroot)
+
+    return return_tag.rstrip()
+
+def save_redirect_from(localroot, root, filename):
+    legacy_from = []
+    os.chdir(root)
+
+    count = 0
+    legacy_from_flag = False
+    tag = "redirect_from"
+    length_tag = len(tag)
+    with open(filename, 'r') as f:
+        for line in f:
+            count += 1
+            # check for the start of the section
+            if line[0:length_tag+1] == tag + ":":
+                legacy_from_flag = True
+
+            # append lines from the legacy section
+            if legacy_from_flag:
+                legacy_from.append(line)
+
+            # check for the end of the header
+            if legacy_from_flag and line[0:3] == "---":
+               legacy_from_flag = False
+               break
+
+    # change back to the local root
+    os.chdir(localroot)
+
+    return legacy_from
+
+def remove_header(localroot, root, filename):
+    nfirstlines = []
+
+    os.chdir(root)
+
+    # count the number of lines
+    count = 0
+    n = 0
+    headerCheck = False
+    with open(filename, 'r') as f:
+        for line in f:
+            count += 1
+
+            # check if the header is actually a header
+            if count > 1 and line[0:3] == "---":
+                headerCheck = True
+                n = count
+
+    # remove the header
+    if headerCheck:
+        with open(filename) as f, open("tmp"+filename, "w") as out:
+            for _ in range(n):
+                nfirstlines.append(next(f))
+            for line in f:
+                out.write(line)
+
+        os.remove(filename)
+        os.rename("tmp"+filename, filename)
+        print(" - Old header removed.")
+
+    # change back to the local root
+    os.chdir(localroot)
+
+    return n
+
+def generate_header(folder, permalink, order, legacy_from, title, description, published, date):
+    header = "---\n"
+    header += "layout: default\n"
+
+    if len(date) > 0:
+        header += "date: " + date + "\n"
+    if len(order) > 0:
+        header += "order: " + str(order) + "\n"
+
+    # add the title and description
+    if len(title) > 0:
+        header += "title: " + title + "\n"
+    if len(description) > 0:
+        header += "description: " + description + "\n"
+
+    header += "permalink: " + permalink + "\n"
+    header += "published: " + published + "\n"
+
+    # include the legacy section
+    if len(legacy_from) > 0:
+        for item in legacy_from:
+            header += str(item)
+    else:
+        header += "---"
+
+    return header
+
+# loop through the entire internal tree
+localroot = os.getcwd()
+
+# generate the index properly speaking
+cardDirs = ["frozen"]
+
+# Index contains the generated content, init it with an empty container
+index = ''
+list_titles = []
+
+for folder in cardDirs:
+    # FolderFlag gets set to true at the first iteration
+    folderFlag = True
+    indexS = 0
+                # walk through the folders with all the cards
+    for root, dirs, files in os.walk(folder):
+        for file in files:
+            if file.endswith(".md"):
+                fileName = os.path.join(root, file)
+                # ignore subsections (.md files that start with _)
+                if file[0] != "_":
+                    print(" > Generating header for: " + fileName)
+
+                    # save order and legacy section
+                    order = save_tag(localroot, root, file, "order")
+                    legacy_from = save_redirect_from(localroot, root, file)
+                    title = save_tag(localroot, root, file, "title")
+                    description = save_tag(localroot, root, file, "description")
+                    permalink = save_tag(localroot, root, file, "permalink")
+                    published = save_tag(localroot, root, file, "published")
+                    date = save_tag(localroot, root, file, "date")
+                    year = date[0:4]
+
+                    # remove the previous header
+                    n = remove_header(localroot, root, file)
+
+                    # generate the header for each card
+                    header = generate_header(folder, permalink, order, legacy_from, title, description, published, date)
+
+                    # add the header properly speaking
+                    line_prepender(fileName, header)
+                    # open file and get the title after the header
+                    list_titles.append({ 'date' : date , 'year': year, 'title': title, 'link': build_link(title, permalink)})
+                    # output
+                    print(" + New header added.")
+                    print("-----------------------")
+
+
+# ordering of cards
+list_titles.sort(key=lambda x: x['date'].split('-'), reverse=True)
+
+# determine the index
+loop_year = list_titles[0]['year']
+
+# add the first year
+index += "\n<h3>" + loop_year + "</h3>\n"
+index += '\n<ul>\n'
+# loop through all pages
+for k in range(len(list_titles)):
+    if list_titles[k]['year'] != loop_year:
+        loop_year = list_titles[k]['year']
+        index += "\n</ul>"
+        index += "\n<h3>" + loop_year + "</h3>\n"
+        index += '\n<ul>\n'
+
+    # add the link properly speaking
+    index += ''.join(list_titles[k]['link'])
+
+index += '\n</ul>\n'
+
+# Read in the file
+indexFile = "frozen.md"
+filedata = ""
+with open(indexFile, 'r') as file :
+    for line in file:
+        filedata += line
+
+        # stop reading once the index place holder has been reached
+        if re.search("<!-- index -->", line):
+            filedata += "[[ index ]]"
+            break
+
+# Replace the target string
+filedata = filedata.replace('[[ index ]]', index)
+
+# Write the file out again
+with open(indexFile, 'w') as file:
+  file.write(filedata)
+
+print("\n > New index generated and saved in " + indexFile)
\ No newline at end of file

.gitlab-ci.yml

@@ -2,11 +2,76 @@
 image: $CI_REGISTRY/r3/docker/jekyll-lcsb:1.8
 
 stages:
+  - prepare
+  - save
   - build
   - deploy
   - backup
   - recovery
 
+.global_settings_mr: &global_settings_mr
+  rules:
+    # run the job for master or develop
+    - if: '$CI_COMMIT_BRANCH == "master" || $CI_COMMIT_BRANCH == "develop"'
+    # run the job for a merge request
+    - if: '$CI_PIPELINE_SOURCE == "merge_request_event"'
+
+.global_settings_mr_no_fork_bot: &global_settings_mr_no_fork_bot
+  rules:
+    # run the job for a merge request, but not from a fork, and not when the commit message has been set by the bot
+    - if: '$CI_PIPELINE_SOURCE == "merge_request_event" && $CI_MERGE_REQUEST_SOURCE_PROJECT_PATH == "R3/r3-pages" && $CI_COMMIT_MESSAGE !~ /tmpBranch/ && $CI_COMMIT_MESSAGE !~ /Update index/'
+
+# prepare
+# ------------------------------------------------------------------------------------
+
+prepare:index:
+  image: python
+  stage: prepare
+  before_script:
+    - pip install natsort
+    - mkdir .tmp
+  script:
+    - python .ci/generateIndex.py
+    - cp frozen.md .tmp/.
+  artifacts:
+    expire_in: 1 day
+    paths:
+      - .tmp
+  <<: *global_settings_mr
+
+# save
+# ------------------------------------------------------------------------------------
+
+save:commitIndex:
+  image:
+    name: alpine/git
+    entrypoint: [""]
+  stage: save
+  before_script:
+    - apk add git-lfs
+    - git fetch --all
+    - url_host=`git remote get-url origin | sed -e "s/https:\/\/gitlab-ci-token:.*@//g"`
+    - git remote set-url origin "https://$GIT_ACCESS_USER:$GIT_ACCESS_TOKEN@${url_host}"
+    - git config user.name $GIT_ACCESS_USER
+    - git config user.email $GIT_ACCESS_EMAIL
+  script:
+    # copy the index and remove the temporary directory
+    - cp .tmp/frozen.md .
+    - rm -rf .tmp
+
+    # commit
+    - git branch -D tmpBranch || true
+    - git checkout -b tmpBranch || true
+    - git add frozen.md || true
+    - git commit -m "Update index" || true
+    - git checkout $CI_COMMIT_REF_NAME || true
+    - git pull origin $CI_COMMIT_REF_NAME || true
+    - git merge tmpBranch --ff || true
+    - git push origin $CI_COMMIT_REF_NAME || true
+    - git branch -D tmpBranch || true
+  <<: *global_settings_mr_no_fork_bot
+
+
 build the website:
   stage: build
   before_script:

Gemfile

@@ -12,7 +12,7 @@ gem "jekyll", "~> 4.0"
 gem "bundler", "> 2.0"
 
 gem "minima", "~> 2.5"
-gem 'jekyll-theme-lcsb-default', '~> 0.4'
+gem 'jekyll-theme-lcsb-default', '~> 0.4.14'
 
 # If you want to use GitHub Pages, remove the "gem "jekyll"" above and
 # uncomment the line below. To upgrade, run `bundle update github-pages`.
@@ -27,9 +27,8 @@ group :jekyll_plugins do
      "~> 0.6"
 
  gem 'jekyll-theme-lcsb-frozen-components',
-     '~> 0.0.2',
      :git => "https://gitlab.lcsb.uni.lu/core-services/jekyll-theme-lcsb-frozen-components.git",
-     :tag => "0.0.2"
+     :tag => "0.0.3"
 
  gem 'jekyll-redirect-from',
      '0.16.0'
@@ -43,3 +42,5 @@ gem "tzinfo-data", platforms: [:mingw, :mswin, :x64_mingw, :jruby]
 gem "wdm", "~> 0.1.1" if Gem.win_platform?
 
 gem 'jekyll-spaceship', "0.10.0"
+
+gem "webrick", "~> 1.7"

_config.yml

@@ -23,8 +23,8 @@ description: >- # this means to ignore newlines until "baseurl:"
 # URL settings that will be used to access on your local machine
 # Note #1: by default you will need to use port 4000 (https://localhost:4000/website) to access the website in your browser running on your machine with `bundle exec jekyll serve`
 # Note #2: the configuration used in GitlabCI is generated in `.gitlab-ci.yml` file automatically for you, if you need to change that - do it there
-baseurl: "/website"
-url: "https://localhost"
+baseurl: "/"
+url: "http://localhost:4000"
 
 banner: default  # When you have custom images, change this setting's value to the name of the folder containing them
 logo: small  # Change to "big" (without quotas) in case of having broad logo

frozen.md

@@ -4,56 +4,60 @@ title: Frozen pages
 order: 2
 permalink: /frozen/
 ---
-
-# Information
-Here you can find project pages that are related to a published scientific paper. Project pages must link to all components referenced in the paper and is not modified after the release of the paper.
-
-This website is under version control on the [LCSB Gitlab](https://gitlab.lcsb.uni.lu/core-services/r3-pages).
-
 # Frozen pages
 
-* **[Modeling Parkinson's disease in midbrain like organoids]({{ "frozen/modeling-parkinsons-disease-in-midbrain-like-organoids" | relative_url }})**
-
-* **[Synapse Alterations Precede Neuronal Damage And Storage Pathology In A Human Cerebral Organoid Model]({{ "frozen/synapse-alterations-precede-neuronal-damage-and-storage-pathology-in-a-human-cerebral-organoid-model" | relative_url }})**
-
-* **[IMP - Integrated Metaomic Pipeline]({{ "frozen/imp" | relative_url }})**
-
-* **[Reproducible generation of human midbrain organoids for in vitro modeling of Parkinson's disease]({{ "frozen/reproducible-generation-of-human-midbrain-organoids-for-in-vitro-modeling-of-parkinsons-disease" | relative_url }})**
-
-* **[SmartR]({{ "frozen/smartr" | relative_url }})** - an open-source platform for interactive visual analytics for translational research data
-
-* **[Single-cell transcriptomics reveals multiple neuronal cell types in human midbrain-specific organoids]({{ "frozen/single-cell-transcriptomics-reveals-multiple-neuronal-cell-types-in-human-midbrain-specific-organoids" | relative_url }})**
-
-* **[Machine learning-assisted neurotoxicity prediction in human midbrain organoids]({{ "frozen/machine-learning-assisted-neurotoxicity-prediction-in-human-midbrain-organoids" | relative_url }})**
-
-* **[Passive controlled flow for neuronal cell culture in 3D microfluidic devices]({{ "frozen/passive-controlled-flow-for-neuronal-cell-culture-in-3d-microfluidic-devices" | relative_url }})**
-
-* **[Using high-content screening technology as a tool to generate single-cell patient-derived gene-corrected isogenic iPS clones for Parkinson’s disease research]({{ "frozen/screening" | relative_url }})**
-
-* **[Clustering and visualizing huge-scale cytometry datasets with GigaSOM.jl]({{ "frozen/gigasom" | relative_url }})**
+Here you can find frozen pages that are related to a published scientific paper. A frozen page regroups all links to all components referenced in the paper and is not modified after the release of the paper.
 
-* **[Mitochondrial morphology provides a mechanism for energy buffering at synapses]({{ "frozen/mitochondrial-morphology-provides-a-mechanism-for-energy-buffering-at-synapses" | relative_url }})**
-
-* **[Retrograde procedural memory in Parkinson's disease: a cross-sectional, case-control study]({{ "frozen/7bwb-aj16" | relative_url }})**
-
-* **[Retrospective Non-target Analysis to Support Regulatory Water Monitoring: From Masses of Interest to Recommendations via in silico workflows]({{ "frozen/40ss-ft75" | relative_url }})**
-
-* **[Identification of tissue-specific and common methylation quantitative trait loci in healthy individuals using MAGAR]({{ "frozen/g9aq-jy72" | relative_url }})**
-
-* **[COBREXA.jl: constraint-based reconstruction andexascale analysis]({{ "frozen/zkcr-bt30" | relative_url }})**
-
-* **[Midbrain organoids mimic early embryonic neurodevelopment and recapitulate LRRK2-G2019S - associated gene expression]({{ "frozen/rc4f-nk07" | relative_url }})**
-
-* **[Functional meta-omics provide critical insights into long and short read assemblies]({{ "frozen/sgzt-ad12" | relative_url }})**
-
-* **[Protein Relative Abundance Quantification Algorithm for 3d fluorescent images from tissue]({{ "frozen/PRAQA" | relative_url }})**
-
-* **[Synaptic decline precedes dopaminergic neuronal loss in human midbrain organoids harboring a triplication of the SNCA gene]({{ "frozen/1yzp-qv41" | relative_url }})**
-
-* **[ A "two-hit" pharmacological seizure model in zebrafish for studying microglia dynamics in the developing epileptic brain]({{ "frozen/77zg-bc41" | relative_url }})**
-
-* **[Method optimization of skin biopsy-derived fibroblast culture for reprogramming into induced pluripotent stem cells (iPSCs)]({{ "frozen/255d-4a98" | relative_url }})**
-
-* **[Meta-analysis of gender-dependent gene expression alterations in Parkinson’s disease]({{ "frozen/hpbx-y095" | relative_url }})**
+This website is under version control on the [LCSB Gitlab](https://gitlab.lcsb.uni.lu/core-services/r3-pages).
 
-* **[Concomitant AD and DLB pathologies shape subfield microglia responses in the hippocampus]({{ "frozen/w2d6-4934" | relative_url }})**
+<!-- index -->
+<h3>2021</h3>
+
+<ul>
+	<li><a href="{{ '/frozen/w2d6-4934' | relative_url }}">Concomitant AD and DLB pathologies shape subfield microglia responses in the hippocampus</a></li>
+	<li><a href="{{ '/frozen/hpbx-y095' | relative_url }}">Meta-analysis of gender-dependent gene expression alterations in Parkinson's disease</a></li>
+	<li><a href="{{ '/frozen/y9k6-xa72' | relative_url }}">The Parkinson's disease associated mutation LRRK2-G2019S alters dopaminergic differentiation dynamics via NR2F1</a></li>
+	<li><a href="{{ '/frozen/77zg-bc41' | relative_url }}">A 'two-hit' pharmacological seizure model in zebrafish for studying microglia dynamics in the developing epileptic brain</a></li>
+	<li><a href="{{ '/frozen/cca2-s098' | relative_url }}">Single cell transcriptomics of human iPSC differentiation dynamics reveal a core network of Parkinson’s disease</a></li>
+	<li><a href="{{ '/frozen/9xkm-3s60' | relative_url }}">Dibac: Distribution-Based Analysis Of Cell Differentiation Identifies Mechanisms Of Cell Fate</a></li>
+	<li><a href="{{ '/frozen/1yzp-qv41' | relative_url }}">Synaptic decline precedes dopaminergic neuronal loss in human midbrain organoids harboring a triplication of the SNCA gene</a></li>
+	<li><a href="{{ '/frozen/sgzt-ad12' | relative_url }}">Functional meta-omics provide critical insights into long and short read assemblies</a></li>
+	<li><a href="{{ '/frozen/255d-4a98' | relative_url }}">Method optimization of skin biopsy-derived fibroblast culture for reprogramming into induced pluripotent stem cells (iPSCs)</a></li>
+	<li><a href="{{ '/frozen/zkcr-bt30' | relative_url }}">COBREXA.jl: constraint-based reconstruction andexascale analysis</a></li>
+	<li><a href="{{ '/frozen/rc4f-nk07' | relative_url }}">Midbrain organoids mimic early embryonic neurodevelopment and recapitulate LRRK2-G2019S - associated gene expression</a></li>
+	<li><a href="{{ '/frozen/g9aq-jy72' | relative_url }}">Identification of tissue-specific and common methylation quantitative trait loci in healthy individuals using MAGAR</a></li>
+	<li><a href="{{ '/frozen/40ss-ft75' | relative_url }}">Retrospective Non-target Analysis to Support Regulatory Water Monitoring: From Masses of Interest to Recommendations via in silico workflows</a></li>
+	<li><a href="{{ '/frozen/cx25-ht49' | relative_url }}">Microglia integration into human midbrain organoids leads to increased neuronal maturation and functionality</a></li>
+	<li><a href="{{ '/frozen/7bwb-aj16' | relative_url }}">Retrograde procedural memory in Parkinson's disease: a cross-sectional, case-control study</a></li>
+
+</ul>
+<h3>2020</h3>
+
+<ul>
+	<li><a href="{{ '/frozen/tnyy-fy53' | relative_url }}">Metadata for the RESOLUTE project in the IMI Data Catalog</a></li>
+	<li><a href="{{ '/frozen/th9v-xt85' | relative_url }}">PRECISESADS: Molecular reclassification to find clinically useful biomarkers for systemic autoimmune diseases</a></li>
+	<li><a href="{{ '/frozen/q3g1-7a85' | relative_url }}">Agent-based SEIR-ICU model for Luxembourg</a></li>
+	<li><a href="{{ '/frozen/c80y-2k58' | relative_url }}">Parkinson's Disease Phenotypes in Patient Neuronal Cultures and Brain Organoids Improved by 2‐Hydroxypropyl‐β‐Cyclodextrin Treatment</a></li>
+	<li><a href="{{ '/frozen/j20h-pa27' | relative_url }}">PaFSe: a Parameter Free Segmentation Approach for 3D Fluorescent Images</a></li>
+	<li><a href="{{ '/frozen/z5vy-fa75' | relative_url }}">Clustering and visualizing huge-scale cytometry datasets with GigaSOM.jl</a></li>
+	<li><a href="{{ '/frozen/lcsb-kcqg-tr55' | relative_url }}">Using High-Content Screening to Generate Single-Cell Gene-Corrected Patient-Derived iPS Clones Reveals Excess Alpha-Synuclein with Familial Parkinson’s Disease Point Mutation A30P</a></li>
+	<li><a href="{{ '/frozen/lcsb-a8hh-1022' | relative_url }}">Passive controlled flow for neuronal cell culture in 3D microfluidic devices</a></li>
+
+</ul>
+<h3>2019</h3>
+
+<ul>
+	<li><a href="{{ '/frozen/lcsb-20191008-01' | relative_url }}">Reproducible generation of human midbrain organoids for in vitro modeling of Parkinson's disease</a></li>
+	<li><a href="{{ '/frozen/lcsb-2019130913-01' | relative_url }}">Synapse alterations precede neuronal damage and storage pathology in a human cerebral organoid model of CLN3-juvenile neuronal ceroid lipofuscinosis</a></li>
+	<li><a href="{{ '/frozen/lcsb-20191309-02' | relative_url }}">Machine learning-assisted neurotoxicity prediction in human midbrain organoids</a></li>
+	<li><a href="{{ '/frozen/lcsb-20190507-01' | relative_url }}">Mitochondrial morphology provides a mechanism for energy buffering at synapses</a></li>
+	<li><a href="{{ '/frozen/lcsb-20190326-01' | relative_url }}">Single-cell transcriptomics reveals multiple neuronal cell types in human midbrain-specific organoids</a></li>
+	<li><a href="{{ '/frozen/lcsb-20192701-01' | relative_url }}">Modeling Parkinson's disease in midbrain-like organoids</a></li>
+
+</ul>
+<h3>2016</h3>
+
+<ul>
+	<li><a href="{{ '/frozen/21vm-kj21' | relative_url }}">IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses</a></li>
+
+</ul>

frozen/1yzp-qv41.md

 ---
 layout: default
+date: 2021-07-09
 order: -1
 title: "Synaptic decline precedes dopaminergic neuronal loss in human midbrain organoids harboring a triplication of the SNCA gene"
 permalink: /frozen/1yzp-qv41
+published: true
 ---
 
-{% rtitle Synaptic decline precedes dopaminergic neuronal loss in human midbrain organoids harboring a triplication of the SNCA gene %}
+{% rtitle {{ page.title }} %}
 Jennifer Modamio, Cláudia Saraiva, Gemma Gomez-Giro, Sarah Nickels, Javier Jarazo, Paul Antony, Silvia Bolognin, Peter Barbuti, Rashi Halder, Christian Jäger, Rejko Krueger, Enrico Glaab, Jens Schwamborn
 {% endrtitle %}
 

frozen/imp.md → frozen/21vm-kj21.md

 ---
 layout: default
+date: 2016-10-18
 order: -1
-title: Imp
-permalink: /frozen/imp
+title: "IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses"
+permalink: /frozen/21vm-kj21
+published: true
+redirect_from:
+ - /frozen/imp
 ---
 
-{% rtitle IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses %}
+{% rtitle {{ page.title }} %}
+
 Please cite the article on [Genome Biology](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1116-8).
 
-Shaman Narayanasamy†, Yohan Jarosz†, Emilie E. L. Muller, Anna Heintz-Buschart, Malte Herold, Anne Kaysen, Cédric C. Laczny, Nicolás Pinel, Patrick May and Paul Wilmes*
+Shaman Narayanasamy, Yohan Jarosz, Emilie E. L. Muller, Anna Heintz-Buschart, Malte Herold, Anne Kaysen, Cédric C. Laczny, Nicolás Pinel, Patrick May and Paul Wilmes*
 {% endrtitle %}
 
 {% rgridblock a-unique-id %}

frozen/255d-4a98.md

 ---
 layout: default
+date: 2021-05-25
 order: -1
-title: Method optimization of skin biopsy-derived fibroblast culture for reprogramming into induced pluripotent stem cells (iPSCs)
+title: "Method optimization of skin biopsy-derived fibroblast culture for reprogramming into induced pluripotent stem cells (iPSCs)"
 permalink: /frozen/255d-4a98
+published: true
 ---
 
 
-{% rtitle Method optimization of skin biopsy-derived fibroblast culture for reprogramming into induced pluripotent stem cells (iPSCs) %}
+{% rtitle {{ page.title }} %}
 
 Kathleen Mommaerts, Camille Bellora, Pauline Lambert, Seval Türkmen, Jens C. Schwamborn, Fay Betsou
 

frozen/40ss-ft75.md

 ---
 layout: default
+date: 2021-03-03
 order: -1
 title: "Retrospective Non-target Analysis to Support Regulatory Water Monitoring: From Masses of Interest to Recommendations via in silico workflows"
 permalink: /frozen/40ss-ft75
+published: true
 ---
 
-{% rtitle Retrospective Non-target Analysis to Support Regulatory Water Monitoring: From Masses of Interest to Recommendations via in silico workflows %}
+{% rtitle {{ page.title }} %}
 Adelene Lai, Randolph R. Singh, Lubomira Kovalova, Oliver Jaeggi, Todor Kondic, Emma L. Schymanski
 {% endrtitle %}
 

frozen/77zg-bc41.md

 ---
 layout: default
+date: 2021-09-03
 order: -1
-title: A two-hit pharmacological seizure model in zebrafish for studying microglia dynamics in the developing epileptic brain
+title: "A 'two-hit' pharmacological seizure model in zebrafish for studying microglia dynamics in the developing epileptic brain"
 permalink: /frozen/77zg-bc41
+published: true
 ---
 
 
-{% rtitle A "two-hit" pharmacological seizure model in zebrafish for studying microglia dynamics in the developing epileptic brain %}
+{% rtitle {{ page.title }} %}
 
 Teresa G. Martins, Remon Soliman, Cristina Donato, Maria Lorena Cordero-Maldonado, Corrado Ameli, Laurent Mombaerts, Alexander Skupin, Francesca Peri, Alexander D. Crawford
 
@@ -18,19 +20,19 @@ Epilepsy is a chronic brain disorder characterized by unprovoked and recurrent s
 
 **Videos demonstrating the phenotypes after KA injection.**
 
-![](assets/77zg-bc41/S1File_Video_PBS-injected.mp4?preload=auto)
+![]({{ "assets/77zg-bc41/S1File_Video_PBS-injected.mp4?preload=auto" | relative_url }})
 
 3 days post-fertilization larvae from the line *Tg(csf1r:Gal4)i186; Tg(UAS.nfsB.mCherry)i149* outcrossed to *nac<sup>w2</sup>* after systemic injection with PBS. The video shows that all the larvae display normal behavior and respond to touch (escape response) upon a soft tail touch with a fine pointer.
 
-![](assets/77zg-bc41/S1File_Video_0.25mM-KA-injected.mp4?preload=auto)
+![]({{ "assets/77zg-bc41/S1File_Video_0.25mM-KA-injected.mp4?preload=auto" | relative_url }})
 
 3 days post-fertilization larvae from the line *Tg(csf1r:Gal4)i186; Tg(UAS.nfsB.mCherry)i149* outcrossed to *nac<sup>w2</sup>* after systemic injection with 0.25 mM KA. The video shows that for some larvae only there is occasional mild whole-body trembling and no escape response upon a soft tail touch with a fine pointer.
 
-![](assets/77zg-bc41/S1File_Video_0.5mM-KA-injected.mp4?preload=auto)
+![]({{ "assets/77zg-bc41/S1File_Video_0.5mM-KA-injected.mp4?preload=auto" | relative_url }})
 
 3 days post-fertilization larvae from the line *Tg(csf1r:Gal4)i186; Tg(UAS.nfsB.mCherry)i149* outcrossed to *nac<sup>w2</sup>* after systemic injection with 0.5 mM KA. The video shows that all larvae display occasional whole-body trembling and movement. Additionally they do not respond to touch (escape response) upon a soft tail touch with a fine pointer.
 
-![](assets/77zg-bc41/S1File_Video_1mM-KA-injected.mp4?preload=auto)
+![]({{ "assets/77zg-bc41/S1File_Video_1mM-KA-injected.mp4?preload=auto" | relative_url }})
 
 3 days post-fertilization larvae from the line *Tg(csf1r:Gal4)i186; Tg(UAS.nfsB.mCherry)i149* outcrossed to *nac<sup>w2</sup>* after systemic injection with 1 mM KA. The video shows that all larvae have occasional whole-body trembling and do not respond to a soft tail touch with a fine pointer.