Fix error links

.gitlab-ci.yml

@@ -16,6 +16,7 @@ stages:
   image: docker:24
   variables:
     CONTEXT: "."
+    DOCKERFILE: "Dockerfile"
   before_script:
     - i=0; while [ "$i" -lt 12 ]; do docker info && break; sleep 5; i=$(( i + 1 )) ; done
     - docker login -u "$CI_REGISTRY_USER" -p "$CI_REGISTRY_PASSWORD" $CI_REGISTRY
@@ -41,9 +42,7 @@ stages:
 build:dev:nuxt:
   extends: .build
   variables:
-    DOCKERFILE: "Dockerfile"
     IMAGE_NAME: "df-wiki"
-    CONTEXT: "./"
   rules:
     - if: $CI_COMMIT_BRANCH != "main"
 

content/2.defense-systems/0.index.md

@@ -11,23 +11,7 @@ The knowledge of anti-phage defense systems is ever expanding. The spectacular i
 
 
 
-::list-systems
----
-systems:
-    - system: Paris
-      dois: 
-        - 10.1101/2021.01.21.427644
-    - system: AbiE
-      dois: 
-        - 10.1093/nar/gkt1419
-    - system: AVAST
-      dois: 
-        - 10.1126/science.aba0372
-    - system: RM
-      dois:
-        - 10.1093/nar/gku734
----
-::
+
 
 
 

content/2.defense-systems/brex.md

@@ -4,13 +4,13 @@ title: BREX
 
 ## Description
 
-BREX (for Bacteriophage Exclusion) is a family of anti-phage defense systems. BREX systems are active against both lytic and lysogenic phages. They allow phage adsorption but block phage DNA replication, and are considered to be [RM](/list_defense_systems/RM)-like systems (1,2). BREX systems are found in around 10% of sequenced microbial genomes (1).
+BREX (for Bacteriophage Exclusion) is a family of anti-phage defense systems. BREX systems are active against both lytic and lysogenic phages. They allow phage adsorption but block phage DNA replication, and are considered to be [RM](/defense-systems/rm)-like systems (1,2). BREX systems are found in around 10% of sequenced microbial genomes (1).
 
 BREX systems can be divided into six subtypes, and are encoded by 4 to 8 genes, some of these genes being mandatory while others are subtype-specific (1).
 
 ## Molecular mechanism
 
-*B. cereus* BREX Type 1 system was reported to methylate target motifs in the bacterial genome (1). The methylation activity of this system has been hypothesized to allow for self from non-self discrimination, as it is the case for Restriction-Modification ([RM)](/list_defense_systems/RM) systems. 
+*B. cereus* BREX Type 1 system was reported to methylate target motifs in the bacterial genome (1). The methylation activity of this system has been hypothesized to allow for self from non-self discrimination, as it is the case for Restriction-Modification ([RM)](/defense-systems/rm) systems. 
 
 However, the mechanism through which BREX Type 1 systems defend against phages is distinct from RM systems, and does not seem to degrade phage nucleic acids (1). 
 

content/2.defense-systems/disarm.md

@@ -6,7 +6,7 @@ title: DISARM
 
 DISARM (Defense Island System Associated with Restriction-Modification) is a defense system widespread in prokaryotes, encoded by a 5-gene cassette. DISARM provides broad protection against double-stranded DNA phages, including siphophages, myophages, and podophages (1,3).
 
- It was reported to restrict incoming phage DNA and methylate the bacterial host DNA, which could be responsible for self from non-self discrimination (1). This suggests a [Restriction-Modification](/list_defense_systems/RM)-like (RM-like) mechanism, yet some pieces of experimental evidence hint that DISARM actually acts through a novel and uncharacterized molecular mechanism (1,2).
+ It was reported to restrict incoming phage DNA and methylate the bacterial host DNA, which could be responsible for self from non-self discrimination (1). This suggests a [Restriction-Modification](/defense-systems/rm)-like (RM-like) mechanism, yet some pieces of experimental evidence hint that DISARM actually acts through a novel and uncharacterized molecular mechanism (1,2).
 
 ## Molecular mechanism
 

content/2.defense-systems/rst_paris.md

@@ -6,7 +6,7 @@ title: Rst_PARIS
 
 PARIS (for Phage Anti-Restriction-Induced System) is a novel anti-phage system. PARIS is found in 4% of prokaryotic genomes. It comprises an ATPase associated with a DUF4435 protein, which can be found either as a two-gene cassette or a single-gene fusion (1).
 
-This system relies on an unknown [Abortive infection](/general_concepts/Abi) mechanism to trigger growth arrest upon sensing a phage-encoded protein (Ocr). Interestingly, the Ocr protein has been found to inhibit R-M systems and BREX systems, making PARIS a suitable defense mechanism against RM resistant and/or BREX resistant phages (1, 2, 3). 
+This system relies on an unknown [Abortive infection](/general-concepts/abortive-infection) mechanism to trigger growth arrest upon sensing a phage-encoded protein (Ocr). Interestingly, the Ocr protein has been found to inhibit R-M systems and BREX systems, making PARIS a suitable defense mechanism against RM resistant and/or BREX resistant phages (1, 2, 3). 
 
 ## Example of genomic structure