These can be a relative link

Most by hand, others with sed: $ sed -i "s#\[http://www.open-bio.org/wiki/Hackathon Hackathons\]#[[Hackathons]]#g" *.mediawiki $ sed -i "s#(see http://www.open-bio.org/wiki/Projects)#(see [[Projects]])#g" *.mediawiki There are other examples, see #9.
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diff --git a/BOSC_2010.mediawiki b/BOSC_2010.mediawiki
@@ -115,7 +115,7 @@ One of the more popular activities at BOSC are the Birds-of-a-Feather sub-meetin
 *# parallelized analysis of possibly terabyte size data sets from next-gen sequencing and mass spec proteomics or 
 *# parallelization of bioinformatics algorithms in general (e.g., the Apache Mahout project).
 : Projects may involve Hadoop (MapReduce API + HDFS) as well as associated open source toolkits (Hbase, Hive, Pig, Cascading, etc.) or other NoSQL non-relational data stores.
-* '''Cloud-based approaches to improving software and data accessibility''' -- The emergence of [http://en.wikipedia.org/wiki/Cloud_computing cloud computing] has made highly scalable cluster computing available to computational biologists. Services such as [http://aws.amazon.com/ec2/ Amazon Elastic Compute Cloud] combined with [http://aws.amazon.com/publicdatasets/#1 publicly available datasets] promise to lower the overhead to participate in large scale data analyses. We are interested in talks focused around how the community can build up resources and datasets for cloud infrastructure, as well as the sharing of insights, and the contribution of implemented workflows.  Current implementations and initiatives are encouraged to submit abstracts for talks and join in the pre-conference [http://www.open-bio.org/wiki/Codefest_2010 Codefest session].
+* '''Cloud-based approaches to improving software and data accessibility''' -- The emergence of [http://en.wikipedia.org/wiki/Cloud_computing cloud computing] has made highly scalable cluster computing available to computational biologists. Services such as [http://aws.amazon.com/ec2/ Amazon Elastic Compute Cloud] combined with [http://aws.amazon.com/publicdatasets/#1 publicly available datasets] promise to lower the overhead to participate in large scale data analyses. We are interested in talks focused around how the community can build up resources and datasets for cloud infrastructure, as well as the sharing of insights, and the contribution of implemented workflows.  Current implementations and initiatives are encouraged to submit abstracts for talks and join in the pre-conference [[Codefest_2010|Codefest session]].
 * '''The Semantic Web in open source bioinformatics''' -- Emerging [http://en.wikipedia.org/wiki/Semantic_Web Semantic Web] technologies promise to improve data interoperability and accessibility.  Seeing these developments as promising for life science researchers who struggle daily with new file formats and incompatible datasets, [http://hackathon3.dbcls.jp/ BioHackathon 2010] focused around current semantic resources and tools for bioinformatics. We solicit session talks from researchers using RDF and related technologies in their research and data analyses, with a special focus on documenting how these tools can contribute to open data access.
 * '''Open Source Software''' -- Open source software that does not fit neatly into the above categories.  
 * '''Lightning Talks''' -- short, 5 minute talks intended to introduce very recent developments, initiate discussion, or highlight resources of interest to BOSC attendees.  Abstracts for Lightning Talks will be accepted up to the first day of BOSC and will be accepted based on space availability and conformance to the Open Source License Requirement.

diff --git a/BOSC_2010_Schedule.mediawiki b/BOSC_2010_Schedule.mediawiki
@@ -140,7 +140,7 @@ Click on the talk title to view the individual abstract as a PDF file.
 |-
 | 6:06-6:15
 | Brad Chapman
-| [Lightning Talk] [http://www.open-bio.org/wiki/Codefest_2010 Codefest 2010 Report]
+| [Lightning Talk] [[Codefest_2010 | Codefest 2010 Report]]
 |-
 | 6:15-6:45
 | &nbsp;

diff --git a/BOSC_2012.mediawiki b/BOSC_2012.mediawiki
@@ -36,7 +36,7 @@ The conference schedule is available '''[[BOSC_2012_Schedule|here as HTML]]''' a
 * '''Genome-scale Data Management''' -- This session will focus on processes and technologies that support the creating, managing and reporting of genomic data. This session is appropriate for discussion of systems that involve components such as (but not limited to) Ensembl and GMOD/Chado data stores, Taverna and Galaxy analysis workflows, and BioMart and InterMine warehouses.
 * '''Linked Data and Translational Knowledge Discovery''' -- Linked Data is an emerging set of conventions on using basic Semantic Web standards (HTTP URIs and [http://dev.isb-sib.ch/projects/uniprot-rdf/ RDF] in particular) to expose, share, and connect data, information, and knowledge online. This session will explore the application of Linked Data and other knowledge-discovery techniques and paradigms to help advance our understanding of human health and disease.
 * '''Software Interoperability''' -- Open Source approaches to integrating the latest bioinformatics tools. Examples of interoperability environments include Galaxy, Cytoscape, caBIG, and myGrid.
-* '''Bioinformatics Open Source Project Updates''' -- This session will feature short talks from ongoing projects describing their recent progress. Abstracts will be solicited from open source projects affiliated with the OBF (see http://www.open-bio.org/wiki/Projects), including the Bio* projects, DAS, BioMOBY, EMBOSS, and GMOD, but any other open-source project will be equally eligible to submit presentations for this session.
+* '''Bioinformatics Open Source Project Updates''' -- This session will feature short talks from ongoing projects describing their recent progress. Abstracts will be solicited from open source projects affiliated with the OBF (see [[Projects]]), including the Bio* projects, DAS, BioMOBY, EMBOSS, and GMOD, but any other open-source project will be equally eligible to submit presentations for this session.
 * '''Panel: Bioinformatics Paper Reviews: Open Standards and Standards of Openness''' -- This panel will cover two interrelated types of openness in bioinformatics paper reviews:
 <ul><ul><li>Shared standards/criteria that all reviewers could use when judging bioinformatics papers.
 <li>The requirement that authors make their software/methods/data available so that reviewers can replicate and evaluate the work described in the paper.</ul>Should bioinformatics reviewers be encouraged--or required--to use a standardized set of review criteria? (Some possible criteria are described [http://ivory.idyll.org/blog/may-12/blog-review-criteria-for-bioinfo.html in this blog post].)  Should bioinformatics journals require authors, as a condition for publication, to release their tools and scripts? Can we develop procedures for fairly and systematically testing bioinformatics software, and should this testing be done openly (rather than secretly by anonymized paper reviewers)? These and other related topics will be discussed by a panel of experienced and opinionated bioinformatics researchers, in conversation with members of the audience.</ul>

diff --git a/BOSC_2012_Schedule.mediawiki b/BOSC_2012_Schedule.mediawiki
@@ -80,7 +80,7 @@ title: BOSC 2012 Schedule
 | (Ian Holmes is sick--instead we will see a short talk on JBrowse by Robert Buels)
 |-
 | 2:38
-| [http://www.slideshare.net/jandot/b-chapman-codefest-bosc2012 Report] on [http://www.open-bio.org/wiki/Codefest_2012 Codefest 2012]
+| [http://www.slideshare.net/jandot/b-chapman-codefest-bosc2012 Report] on [[Codefest 2012]]
 | Brad Chapman
 |-
 | 2:45
@@ -120,7 +120,7 @@ title: BOSC 2012 Schedule
 | Sophia Cheng 
 |-
 | 5:20
-| Introduction to the [http://www.open-bio.org/wiki/Main_Page Open Bioinformatics Foundation]
+| Introduction to the [[Main_Page|Open Bioinformatics Foundation]]
 | Hilmar Lapp (President, Open Bioinformatics Foundation)
 |-
 | 5:30

diff --git a/BOSC_2013.mediawiki b/BOSC_2013.mediawiki
@@ -48,7 +48,7 @@ The conference schedule is available '''[[BOSC_2013_Schedule|here as HTML]]''' a
 * '''Visualization''' -- Current data acquisition technologies are moving us more and more towards a "data first, hypothesis later" paradigm for scientific research. As a result, data visualization and visual analytics are of increasing importance. This session focuses on approaches for interactive as well as static visual representations of biomedical data, ranging from exploration to explanation.
 * '''Software Interoperability''' -- This session covers Open Source approaches to integrating the latest bioinformatics tools. Building flexible, reproducible workflows with connected tools is essential to modern bioinformatics. The goal of this session is to investigate how we can increase tool connectivity and help communities work better together.
 * '''Translational Bioinformatics''' -- This session will explore applications of biological and medical informatics to the development of personalized healthcare, therapies, and a better understanding of human health and disease. Topics include the analysis of large scale population and family sequencing data, bioinformatics methodologies for clinical research, and tools for discovering clinically useful associations in human databases. We especially welcome work that bridges the gap between research and patients, making analysis tools available and understandable for non-scientists.
-* '''Bioinformatics Open Source Project Updates''' -- This session will feature short talks from ongoing projects describing their recent progress. Abstracts will be solicited from open source projects affiliated with the OBF (see http://www.open-bio.org/wiki/Projects), including the Bio* projects, DAS, BioMOBY, EMBOSS, and GMOD, but any other open-source project will be equally eligible to submit abstracts for this session.
+* '''Bioinformatics Open Source Project Updates''' -- This session will feature short talks from ongoing projects describing their recent progress. Abstracts will be solicited from open source projects affiliated with the OBF (see [[Projects]]), including the Bio* projects, DAS, BioMOBY, EMBOSS, and GMOD, but any other open-source project will be equally eligible to submit abstracts for this session.
 * '''[[BOSC_Panel_2013|Panel: Strategies for funding and maintaining open source software]]'''
 
 == Submitting Abstracts ==

diff --git a/BOSC_2013_Schedule.mediawiki b/BOSC_2013_Schedule.mediawiki
@@ -172,7 +172,7 @@ You can also:
 | Brad Chapman
 |-
 | 9:00
-| [http://www.open-bio.org/wiki/Main_Page Open Bioinformatics Foundation:]  A Community For, By, and Of You ([http://www.slideshare.net/hlapp/obf-address-bosc2013 SlideShare] [http://www.youtube.com/watch?v=DiReTX3FoLM YouTube])
+| [[Main_Page|Open Bioinformatics Foundation]]:  A Community For, By, and Of You ([http://www.slideshare.net/hlapp/obf-address-bosc2013 SlideShare] [http://www.youtube.com/watch?v=DiReTX3FoLM YouTube])
 | Hilmar Lapp (President, Open Bioinformatics Foundation)
 |-
 | 9:15

diff --git a/BOSC_2014.mediawiki b/BOSC_2014.mediawiki
@@ -8,7 +8,7 @@ __NOTOC__
 
 The 15th Annual Bioinformatics Open Source Conference (BOSC 2014) was held at the Hynes Convention Center in Boston on July 11-12, right before [https://www.iscb.org/ismb2014 ISMB 2014] as one of the official ISMB SIG satellite meetings. Feedback welcome via email [email protected] or [https://twitter.com/OBF_BOSC @OBF_BOSC on Twitter].
 
-'''[http://www.open-bio.org/wiki/BOSC_2014_Schedule Complete Schedule]''' (with links to posters, slides and videos of the talks)
+'''[[BOSC_2014_Schedule|Complete Schedule]]''' (with links to posters, slides and videos of the talks)
 
 == Media ==
 
@@ -25,7 +25,7 @@ Brad Chapman's [http://smallchangebio.wordpress.com/2014/07/11/notes-bioinformat
 * July 9-10, 2014: [[Codefest 2014]], Boston, MA
 * July 11-12, 2014: BOSC 2014, Boston, MA
 * July 12-16, 2014: [http://www.iscb.org/ismb2014 ISMB 2014], Boston, MA
-* September 18-19, 2014: [http://www.open-bio.org/wiki/EU-Codefest_2014 EU-Codefest 2014], Cambridge, UK
+* September 18-19, 2014: [[EU-Codefest 2014]], Cambridge, UK
 
 == Overview ==
 
@@ -69,7 +69,7 @@ We are grateful to [http://www.google.com/ Google] for their generous support fo
 * '''Genome-scale Data and Beyond''' -- encompasses software and other tools designed for managing, exploring, and analyzing large-scale data to address research questions, such as genome assembly, variant prediction, eQTL analysis, phylogenomics, and epigenetics.
 * '''Visualization''' -- focuses on approaches for interactive as well as static visual representations of biomedical data, ranging from exploration to explanation.
 * '''Translational Bioinformatics''' -- explores applications of biological and medical informatics to the development of personalized healthcare, therapies, and a better understanding of human health and disease. Topics include the analysis of large scale population and family sequencing data, bioinformatics methodologies for clinical research, and tools for discovering clinically useful associations in human databases.
-* '''Bioinformatics Open Source Project Updates''' -- features short talks from ongoing projects describing their recent progress. Abstracts will be solicited from open source projects affiliated with the OBF (see http://www.open-bio.org/wiki/Projects), including the Bio* projects, DAS, BioMOBY, EMBOSS, and GMOD, but any other open-source project will be equally eligible to submit abstracts for this session.
+* '''Bioinformatics Open Source Project Updates''' -- features short talks from ongoing projects describing their recent progress. Abstracts will be solicited from open source projects affiliated with the OBF (see [[Projects]]), including the Bio* projects, DAS, BioMOBY, EMBOSS, and GMOD, but any other open-source project will be equally eligible to submit abstracts for this session.
 * '''Panel''': Reproducibility: Rewards and Challenges
 
 == Keynote Speakers ==
@@ -79,7 +79,7 @@ This year's keynote speakers will be Philip Bourne (NIH) and C. Titus Brown (Mic
 
 == Submitting Abstracts ==
 
-The deadline for submitting abstracts to be considered for full talks was Friday, April 4, 2014.  We still have a few spots reserved for last-minute posters--[http://www.open-bio.org/wiki/BOSC_Abstract_Submission submit your abstract here].
+The deadline for submitting abstracts to be considered for full talks was Friday, April 4, 2014.  We still have a few spots reserved for last-minute posters -- [[BOSC_Abstract_Submission|submit your abstract here]].
 
 == Organizing Committee ==
 

diff --git a/BOSC_2014_Schedule.mediawiki b/BOSC_2014_Schedule.mediawiki
@@ -63,7 +63,7 @@ See [[Codefest_2014 | Codefest 2014]] for details.
 | John Chilton
 |-
 | 12:15-12:30
-| [http://www.open-bio.org/wiki/Main_Page Open Bioinformatics Foundation (OBF) update] ([https://youtu.be/1oSTb8ZAxec video])
+| [[Main_Page|Open Bioinformatics Foundation (OBF) update]] ([https://youtu.be/1oSTb8ZAxec video])
 | Hilmar Lapp (OBF President)
 |-
 | '''12:30-13:30'''

diff --git a/BOSC_2015.mediawiki b/BOSC_2015.mediawiki
@@ -85,7 +85,7 @@ We welcome submissions relating to all aspects of bioinformatics and open scienc
 * '''Data Science''' -- encompasses software and approaches to managing, exploring, and analyzing large-scale data to address research questions, such as genome assembly, variant prediction, eQTL analysis, phylogenomics, and epigenetics.
 * '''Visualization''' -- focuses on approaches for interactive as well as static visual representations of biomedical data, ranging from exploration to explanation.
 * '''Translational Bioinformatics''' -- explores applications of biological and medical informatics to the development of personalized healthcare, therapies, and a better understanding of human health and disease. Topics include the analysis of large scale population and family sequencing data, bioinformatics methodologies for clinical research, and tools for discovering clinically useful associations in human databases.
-* '''Bioinformatics Open Source Libraries and Projects''' -- features short talks from new or ongoing projects describing their recent progress. Abstracts will be solicited from open source projects affiliated with the OBF (see http://www.open-bio.org/wiki/Projects), including the Bio* projects, DAS, BioMOBY, EMBOSS, and GMOD, but any other open-source project will be equally eligible to submit abstracts for this session.
+* '''Bioinformatics Open Source Libraries and Projects''' -- features short talks from new or ongoing projects describing their recent progress. Abstracts will be solicited from open source projects affiliated with the OBF (see [[Projects]]), including the Bio* projects, DAS, BioMOBY, EMBOSS, and GMOD, but any other open-source project will be equally eligible to submit abstracts for this session.
 * '''[[BOSC_2015_Panel|Panel: Open Source, Open Door: increasing diversity in the bioinformatics open source community.]]''' ''Chair'': Monica Munoz-Torres. ''Panelists'': Holly Bik, Michael R. Crusoe, Aleksandra Pawlik, Jason Williams.
 
 [[Image:EwanBirney2.jpg|120px|right|Ewan Birney]]

diff --git a/BOSC_2018.mediawiki b/BOSC_2018.mediawiki
@@ -40,7 +40,7 @@ The [https://gccbosc2018.sched.com/directory/speakers BOSC keynote speakers] wil
 [[File:Gcc-bosc-2018-logo_boxed_300.png|100px|left|GCCBOSC 2018|link=https://gccbosc2018.sched.com/]]
 BOSC has been a part of [https://www.iscb.org/ismb2018 ISMB] since its inception, and we greatly value our
 relationships with the ISCB management and the ISMB community.
-[http://www.open-bio.org/wiki/BOSC_2017 BOSC 2017], which was part of
+[[BOSC 2017]], which was part of
 [https://www.iscb.org/ismbeccb2017 ISMB/ECCB 2017] in Prague, was an
 exciting and successful meeting.
 

diff --git a/Codefest_2010.mediawiki b/Codefest_2010.mediawiki
@@ -7,7 +7,7 @@ OpenBio Codefest 2010 will take place July 7th and 8th, 2010 in conjunction with
 == Goals ==
 
 OpenBio projects are typically coordinated remotely, with users from all over the world contributing and organizing themselves through mailing lists and IRC chats. Additionally, contributors work on these projects in their spare time, coordinating improving the projects with their day jobs and life outside of the computer.
-The objective of the Codefest is to give these talented developers a chance to be fully focused on the projects for a few days, interacting in real time. Previous [http://www.open-bio.org/wiki/Hackathon Hackathons] have been immensely successful at producing new high quality code and innovative project developments.
+The objective of the Codefest is to give these talented developers a chance to be fully focused on the projects for a few days, interacting in real time. Previous [[Hackathons]] have been immensely successful at producing new high quality code and innovative project developments.
 
 The general aim of the Codefest is improving the accessibility, functionality and interoperability of the existing libraries. The specific goals are determined based on the interests of attending members and inputs of sponsors. Some current areas of topic discussion are:
 

diff --git a/Codefest_2011.mediawiki b/Codefest_2011.mediawiki
@@ -9,7 +9,7 @@ This is a follow-up to the extremely successful and fun [[Codefest 2010]] in Bos
 == Goals ==
 
 OpenBio projects are typically coordinated remotely, with users from all over the world contributing and organizing themselves through mailing lists and IRC chats. Additionally, contributors work on these projects in their spare time, coordinating improving the projects with their day jobs and life outside of the computer.
-The objective of the Codefest is to give these talented developers a chance to be fully focused on the projects for a few days, interacting in real time. Previous [http://www.open-bio.org/wiki/Hackathon Hackathons] have been immensely successful at producing new high quality code and innovative project developments.
+The objective of the Codefest is to give these talented developers a chance to be fully focused on the projects for a few days, interacting in real time. Previous [[Hackathons]] have been immensely successful at producing new high quality code and innovative project developments.
 
 The goals for the two days are determined entirely by developers. We welcome your input. Please add your thoughts to the shared Google document: