Removing illegal characters from wiki page titles

The most frequent change was replacing ':' with '_'. A permlink was
added to these pages to prevent the URL from changes, as suggested in
jekyll/jekyll#5284

_wikis/Andreas_Draeger.md

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+---
+title: Andreas Dräger
+permalink: Andreas Dräger
+tags:
+ - People
+---
+
+Andreas Dräger is a PhD student at the [Center for Bioinformatics
+(ZBIT)](http://www-ra.informatik.uni-tuebingen.de) in Tübingen, Germany.
+During his master thesis at the [Martin-Luther-University
+Halle-Wittenberg](http://www.uni-halle.de/MLU/index_e.htm) he improved
+the storage of taxonomic information in BioSQL databases and implemented
+sequence alignment algorithms such as the Needleman-Wunsch- and the
+Smith-Waterman-Algorithm for global or local alignment, respectively.

_wikis/Annotations_List.md

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+---
+title: Annotations:List
+permalink: wikis/Annotations%3AList
+---
+
+How do I List the Annotations in a Sequence?
+--------------------------------------------
+
+When you read in a annotates sequence file such as GenBank or EMBL there
+is a lot more detailed information in there than just the raw sequence.
+If the information has a sensible location then it ends up as a Feature.
+If it is more generic such as the species name then the information ends
+up as Annotations.
+
+BioJava Annotation objects are a bit like Map objects and they contian
+key value mappings.
+
+Below is the initial portion of an EMBL file
+
+    ID   AY130859   standard; DNA; HUM; 44226 BP.
+    XX
+    AC   AY130859;
+    XX
+    SV   AY130859.1
+    XX
+    DT   25-JUL-2002 (Rel. 72, Created)
+    DT   25-JUL-2002 (Rel. 72, Last updated, Version 1)
+    XX
+    DE   Homo sapiens cyclin-dependent kinase 7 (CDK7) gene, complete cds.
+    XX
+    KW   .
+    XX
+    OS   Homo sapiens (human)
+    OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
+    OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
+    XX
+    RN   [1]
+    RP   1-44226
+    RA   Rieder M.J., Livingston R.J., Braun A.C., Montoya M.A., Chung M.-W.,
+    RA   Miyamoto K.E., Nguyen C.P., Nguyen D.A., Poel C.L., Robertson P.D.,
+    RA   Schackwitz W.S., Sherwood J.K., Witrak L.A., Nickerson D.A.;
+    RT   ;
+    RL   Submitted (11-JUL-2002) to the EMBL/GenBank/DDBJ databases.
+    RL   Genome Sciences, University of Washington, 1705 NE Pacific, Seattle, WA
+    RL   98195, USA
+    XX
+    CC   To cite this work please use:  NIEHS-SNPs, Environmental Genome
+    CC   Project, NIEHS ES15478, Department of Genome Sciences, Seattle, WA
+    CC   (URL: http://egp.gs.washington.edu).
+
+The following program reads an EMBL file and lists its Annotation
+properties. The output of this program on the above file is listed below
+the program.
+
+```java import java.io.\*; import java.util.\*;
+
+import org.biojava.bio.\*; import org.biojava.bio.seq.\*; import
+org.biojava.bio.seq.io.\*;
+
+public class ListAnnotations {
+
+` public static void main(String[] args) {`
+
+`   try {`  
+`     //read in an EMBL Record`  
+`     BufferedReader br = new  BufferedReader(new FileReader(args[0]));`  
+`     `  
+`     //for each sequence list the annotations`  
+`     for(SequenceIterator seqs = SeqIOTools.readEmbl(br); seqs.hasNext(); ){`  
+`       Annotation anno = seqs.nextSequence().getAnnotation();`
+
+`       //print each key value pair`  
+`       for (Iterator i = anno.keys().iterator(); i.hasNext(); ) {`  
+`         Object key = i.next();`  
+`         System.out.println(key +" : "+ anno.getProperty(key));`  
+`       }`  
+`     }`  
+`   }`  
+`   catch (Exception ex) {`  
+`     ex.printStackTrace();`  
+`   }`  
+` }`
+
+} ```
+
+Program Output
+
+    RN : [1]
+    KW : .
+    RL : [Submitted (11-JUL-2002) to the EMBL/GenBank/DDBJ databases., Genome Sciences, University of Washington, 1705 NE Pacific, Seattle, WA, 98195, USA]
+    embl_accessions : [AY130859]
+    DE : Homo sapiens cyclin-dependent kinase 7 (CDK7) gene, complete cds.
+    SV : AY130859.1
+    AC : AY130859;
+    FH : Key Location/Qualifiers
+    XX :
+    OC : [Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;, Eutheria; Primates; Catarrhini; Hominidae; Homo.]
+    RA : [Rieder M.J., Livingston R.J., Braun A.C., Montoya M.A., Chung M.-W.,, Miyamoto K.E., Nguyen C.P., Nguyen D.A., Poel C.L., Robertson P.D.,, Schackwitz W.S., Sherwood J.K., Witrak L.A., Nickerson D.A.;]
+    ID : AY130859 standard; DNA; HUM; 44226 BP.
+    DT : [25-JUL-2002 (Rel. 72, Created), 25-JUL-2002 (Rel. 72, Last updated, Version 1)]
+    CC : [To cite this work please use: NIEHS-SNPs, Environmental Genome, Project, NIEHS ES15478, Department of Genome Sciences, Seattle, WA, (URL: http://egp.gs.washington.edu).]
+    RT : ;
+    OS : Homo sapiens (human)
+    RP : 1-44226