Wednesday 19 February 2014

In the ERA of science communication, Why you need Twitter, Professional Blog and ImpactStory?

Where is the information? Where are the scientifically relevant results? Where are the good ideas? Are these things (only) in journals? I usually prefer to write about bioinformatics and how we should include, annotate and cite our bioinformatics tools inside research papers (The importance of Package Repositories for Science and Research, The problem of in-house tools); but this post represents my take on the future of scientific publications and their dissemination based on the manuscript “Beyond the paper” (1).

In the not too distant future, today’s science journals will be replaced by a set of decentralized, interoperable services that are built on a core infrastructure of open data and evolving standards — like the Internet itself. What the journal did in the past for a single article, the social media and internet resources are doing for the entire scholarly output. We are now immersed in a transition to another science communication system— one that will tap on Web technology to significantly improves dissemination. I prefer to represent the future of science communication by a block diagram where the four main components: (i) Data, (ii) Publications, (iii) Dissemination and (iv) Certification/Reward are completely interconnected:

Friday 7 February 2014

Solving Invalid signature in JNLP

I have this error each time i run my jnlp:

invalid SHA1 signature file digest for

I found some discussions about possible solutions:

http://stackoverflow.com/questions/8176166/invalid-sha1-signature-file-digest

http://stackoverflow.com/questions/11673707/java-web-start-jar-signing-issue

But he problem was still there. I solved the problem using plugin option (<unsignAlreadySignedJars>true</unsignAlreadySignedJars>) and removing previous signatures to avoid possible signature duplications:



  <plugin>
     <groupId>org.codehaus.mojo.webstart</groupId>
       <artifactId>webstart-maven-plugin</artifactId>
         <executions>
           <execution>
             <id>jnlp-building</id>
             <phase>package</phase>
               <goals>
                 <goal>jnlp</goal>
               </goals>
            </execution>
         </executions>
         <configuration>
           <!-- Include all the dependencies -->
           <excludeTransitive>false</excludeTransitive>
           <unsignAlreadySignedJars>true</unsignAlreadySignedJars>
           <verbose>true</verbose>
           <verifyjar>true</verifyjar>
           <!-- The path where the libraries are stored -->
           <libPath>lib</libPath>
           <jnlp>
             <inputTemplate>webstart/jnlp-template.vm</inputTemplate>
             <outputFile>ProteoLimsViewer.jnlp</outputFile>
             <mainClass>cu.edu.cigb.biocomp.proteolims.gui.ProteoLimsViewer</mainClass>
           </jnlp>
           <sign>
             <keystore>keystorefile</keystore>
             <alias>proteolimsviewer</alias>
             <storepass>password</storepass>
             <keypass>password</keypass>
             <keystoreConfig>
               <delete>false</delete>
               <gen>false</gen>
             </keystoreConfig>
           </sign>
              <!-- building process -->
              <pack200>false</pack200>
              <verbose>true</verbose>
         </configuration>
     </plugin>