https://sourceforge.net/p/insilico-fragmentation/wiki/Home/Recent changes to HomeenTue, 30 May 2017 17:36:27 -0000https://sourceforge.net/p/insilico-fragmentation/wiki/Home/<div class="markdown_content"><pre>--- v1 +++ v2 @@ -1,8 +1,24 @@ -Welcome to your wiki! +**When to use voting/consensus model?** -This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage]. +Voting/consensus model utilizes outputs of 4 software that aid metabolites' structure elucidation: -The wiki uses [Markdown](/p/insilico-fragmentation/wiki/markdown_syntax/) syntax. +[MetFrag](http://c-ruttkies.github.io/MetFrag/projects/metfragcl/) +[CFM-ID](https://sourceforge.net/projects/cfm-id/) +[MAGMa+](https://github.com/savantas/MAGMa-plus) +[MS-FINDER](http://prime.psc.riken.jp/MetabolomicsSoftware/MS-FINDER/index.html) -[[members limit=20]] -[[download_button]] +This means that before using voting/consensus model you will need to use all or some of the software mentioned above. Results (output) of each software will be used as an input for voting/consensus which will then re-order and re-rank the candidates list by using two options: + +* in silico fragmentation only +* in silico fragmentation plus database boosting + +**How to run voting/consensus model?** + +1. Downoload input.zip, output.zip, properties file and the latest .jar version from here +2. Exctract all the files into a working folder. +3. Open file named "application properties" in Notepad and follow the documentation for usage. +4. Depending on which software combination you are interested in you can select/deselect the relevant ones. +5. Save the file and run the application using command line. +6. Execution: This is the line you need to use in order to run the .jar file from the command line: +java -jar comparative-analysis-0.1.2.jar +Results of voting/consensus model are calculated as top hit, top 5, top 10 and top 20. </pre> </div>Ivana BlazenovicTue, 30 May 2017 17:36:27 -0000https://sourceforge.net33c5dc8527368102f583dea6617ebfc17c670182https://sourceforge.net/p/insilico-fragmentation/wiki/Home/<div class="markdown_content"><p>Welcome to your wiki!</p> <p>This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: <span>[SamplePage]</span>.</p> <p>The wiki uses <a class="" href="/p/insilico-fragmentation/wiki/markdown_syntax/">Markdown</a> syntax.</p> <p></p><h6>Project Members:</h6> <ul class="md-users-list"> <li><a href="/u/ivanablazenovic/">Ivana Blazenovic</a> (admin)</li> </ul><br/> <p><span class="download-button-592dab714d00633e159f6626" style="margin-bottom: 1em; display: block;"></span></p><p></p></div>Ivana BlazenovicTue, 30 May 2017 17:27:13 -0000https://sourceforge.net81830c17d82dbceadeeb0390f0308876da4eb720