Changeset 1975

Timestamp:

May 15, 2013, 1:20:50 PM (10 years ago)

Author:

Nicklas Nordborg

Message:

References #485 and #479. Only use 1 decimal in lab protocols for pooling. Use the rounded values when calculating molarity and other values for the pool.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/libprep/create_pools.jsp (modified) (4 diffs)
• resources/libprep/pool_protocol2.jsp (modified) (11 diffs)
• src/net/sf/basedb/reggie/Reggie.java (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/PoolServlet.java (modified) (6 diffs)

extensions/net.sf.basedb.reggie/trunk/resources/libprep/create_pools.jsp

@@ -146 +146 @@
         tmp.volume = lib.volume;
         tmp.eb = lib.eb;
-        tmp.extraMixFactor = lib.extraMixFactor;
+        tmp.mixFactor = lib.mixFactor;
         poolInfo.libs[poolInfo.libs.length] = tmp;
       }
@@ -315 +315 @@
     }
 
-    if (lib.extraMixFactor)
+    if (lib.mixFactor > 1.001)
     {
       // Larger mix than default
-      var mixedVolume = (lib.volume+lib.eb)*(1+lib.extraMixFactor);
+      var mixedVolume = (lib.volume+lib.eb)*(lib.mixFactor);
       remarks[remarks.length] = 'Mix ' + Numbers.formatNumber(mixedVolume, 0) + 'µl';
     }
@@ -353 +353 @@
       if (lib)
       {
-        poolMolarity += Math.min(lib.molarity, TARGET_MOLARITY_IN_POOL);
+        poolMolarity += Math.min(lib.molarity, lib.mixMolarity);
         poolVolume += TARGET_VOLUME_IN_POOL_PER_LIB;
         numLibs++;
@@ -392 +392 @@
       var name = lib.name;
       var i = name.indexOf('.m');
-      var mixFactor = 1+lib.extraMixFactor;
+      var mixFactor = lib.mixFactor;
       var displayName = name.substring(0, i)+'.<br>&nbsp;'+name.substring(i);
       text += '<div class="lib">'+displayName+'</div>';
       text += '<span class="barcode">'+lib.barcode.name+'</span>';
       text += '<span class="molarity">'+Numbers.formatNumber(lib.molarity, 2)+'nM</span>';
-      text += '<span class="volume">'+Numbers.formatNumber(lib.volume*mixFactor, 2) + 'µl</span>';
-      text += '<span class="eb">'+Numbers.formatNumber(lib.eb*mixFactor, 2)+'µl</span>';
+      text += '<span class="volume">'+Numbers.formatNumber(lib.volume*mixFactor, 1) + 'µl</span>';
+      text += '<span class="eb">'+Numbers.formatNumber(lib.eb*mixFactor, 1)+'µl</span>';
       text += '<div class="remarks">'+ lib.remarks.join('; ') + '</div>';
     }

extensions/net.sf.basedb.reggie/trunk/resources/libprep/pool_protocol2.jsp

@@ -212 +212 @@
       }
   
-      if (lib.extraMixFactor)
+      if (lib.mixFactor > 1.001)
       {
         // Larger mix than default
-        var mixedVolume = (lib.volume+lib.eb)*(1+lib.extraMixFactor);
+        var mixedVolume = (lib.volume+lib.eb)*(lib.mixFactor);
         remarks[remarks.length] = 'Mix ' + Numbers.formatNumber(mixedVolume, 0) + 'µl';
       }
@@ -266 +266 @@
         }
 
-        addColumn(tr, "lib", lib.name);
-        addColumn(tr, "remain", Numbers.formatNumber((lib.remainingQuantity+lib.usedQuantity)*1000, 2));
-        addColumn(tr, "molarity", Numbers.formatNumber(lib.molarity, 2));
+        addColumn(tr, 'lib', lib.name);
+        addColumn(tr, 'remain', Numbers.formatNumber((lib.remainingQuantity+lib.usedQuantity)*1000, 2));
+        addColumn(tr, 'molarity', Numbers.formatNumber(lib.molarity, 2));
         <%
         if (libPlate==null)
         {
           %>
-          addColumn(tr, "workplate", well.bioPlate.name + ' ' + well.location);
+          addColumn(tr, 'workplate', well.bioPlate.name + ' ' + well.location);
           <%
         }
@@ -279 +279 @@
         {
           %>
-          addColumn(tr, "workplate", well.location);
+          addColumn(tr, 'workplate', well.location);
           <%
         }
         %>
-        var mixFactor = 1+(lib.extraMixFactor || 0);
-        addColumn(tr, "mix", '<span class="volume">'+Numbers.formatNumber(lib.volume*mixFactor, 2)+'</span>+<span class="eb">'+Numbers.formatNumber(lib.eb*mixFactor, 2)+'</span>');
+        var mixFactor = lib.mixFactor || 1.0;
+        addColumn(tr, 'volume', Numbers.formatNumber(lib.volume*mixFactor, 1));
+        addColumn(tr, 'eb', Numbers.formatNumber(lib.eb*mixFactor, 1));
         addColumn(tr, "remarks", lib.remarks.join('; '));
         tbody.appendChild(tr);
@@ -296 +297 @@
   function addColumn(tr, className, html)
   {
-    
     var td = document.createElement('td');
     td.className = className;
     td.innerHTML = html;
     tr.appendChild(td);
-    
   }
   
@@ -308 +307 @@
     Plate.init(8, 12, schema, WellPainter);
     
-    for (var i = 0; i < pools.length; i++)
-    {
-      var pool = pools[i];
-      POOL_NAMES[i] = pool.name;
-      for (var j = 0; j < pool.libraries.length; j++)
-      {
-        var lib = pool.libraries[j];
+    for (var poolNo = 0; poolNo < pools.length; poolNo++)
+    {
+      var pool = pools[poolNo];
+      POOL_NAMES[poolNo] = pool.name;
+      for (var libNo = 0; libNo < pool.libraries.length; libNo++)
+      {
+        var lib = pool.libraries[libNo];
         var well = lib.bioWell;
         Plate.getWell(well.row, well.column).setExtract(lib);
@@ -324 +323 @@
     PoolSchema.buildPoolTableRow(schema, 12);
     Main.show('plateview');
+    
+    
+    for (var poolNo = 0; poolNo < pools.length; poolNo++)
+    {
+      var pool = pools[poolNo];
+      //setInnerHTML('molarity.'+pool.id, Numbers.formatNumber(pool.molarity, 2) + ' nM; ' + Numbers.formatNumber(1000*pool.originalQuantity / pool.conc, 0)+' µl');
+
+      var poolData = '<div class="pool-data">';
+      poolData += Numbers.formatNumber(pool.molarity, 2)+'nM; ';
+      poolData += Numbers.formatNumber(1000*pool.originalQuantity / pool.conc, 0) + 'µl';
+      poolData += '</div>';
+      document.getElementById('pool.'+poolNo).innerHTML = POOL_NAMES[poolNo] + poolData;
+
+    }
   }
 
@@ -349 +362 @@
       {
         var name = lib.name;
-        var mixFactor = 1+(lib.extraMixFactor || 0);
+        var mixFactor = lib.mixFactor || 1.0;
         var i = name.indexOf('.m');
         text += '<div class="lib">'+name.substring(0, i)+'.<br>&nbsp;'+name.substring(i)+'</div>';
@@ -478 +491 @@
   }
 
-  .listview .mix
-  {
-    width: 8em;
+  .listview .volume
+  {
+    width: 3.5em;
     padding-right: 0.5em;
     text-align: right;
-  }
-  
-  .listview .empty .mix
-  {
-    visibility: hidden;
-  }
-  
-  .listview .volume
-  {
     color: #C80000;
-    padding-right: 3px;
   }
   
   .listview .eb
   {
+    width: 3.5em;
+    padding-right: 0.5em;
+    text-align: right;
     color: #0000C8;
-    padding-left: 3px;
   }
   
@@ -546 +551 @@
     color: #C80000;
     font-style: italic;
+  }
+  #plateview .pool-data
+  {
+    font-weight: normal;
   }
   </style>
@@ -620 +629 @@
           <th>DNA</th>
           <th class="workplate">Work</th>
-          <th>2nM, 5/10µl</th>
+          <th colspan="2">2nM, 5/10µl</th>
           <th></th>
         </tr>
@@ -629 +638 @@
           <th class="workplate">plate</th>
           <th>(µl)</th>
+          <th>EB</th>
           <th>Remarks</th>
         </tr>

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/Reggie.java

@@ -156 +156 @@
   }
   
+  /**
+    Round a floating point value to a given number of decimals.
+    @since 2.12
+  */
+  public static float round(float value, int decimals)
+  {
+    double factor = Math.pow(10, decimals);
+    return (float)(Math.round(factor * value) / factor);
+  }
+  
 }

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/PoolServlet.java

@@ -67 +67 @@
   
   /**
-    Percentage to increase the mix when making an extra large mix.
-    In the common case 1.0 means mixing 10µl instead of 5µl. But, only
+    Factor to apply when making an extra large mix.
+    In the common case 2.0 means mixing 10µl instead of 5µl. But, only
     5µl is used for the pool and the remaining 5µl is saved in a temporary
     location.
   */
-  private static final float EXTRA_LARGE_MIX_FACTOR = 1.0f;
+  private static final float EXTRA_LARGE_MIX_FACTOR = 2.0f;
   
   
@@ -358 +358 @@
             
             // 
-            float extraMixFactor = ((Number)jsonLib.get("extraMixFactor")).floatValue();
+            float mixFactor = ((Number)jsonLib.get("mixFactor")).floatValue();
             float usedQuantityForExtra = 0f;
-            if (extraMixFactor > 0)
+            if (mixFactor > 1.001)
             {
               // Create 'dil' extract for keeping track of remaining quantity that has been mixed
-              float usedVolumeForExtra = extraMixFactor * usedVolumeForPool;
+              float usedVolumeForExtra = (mixFactor - 1) * usedVolumeForPool;
               usedQuantityForExtra = usedVolumeForExtra * usedConc / 1000;
               Extract dil = Extract.getNew(dc);
@@ -375 +375 @@
               dil.setOriginalQuantity(usedQuantityForExtra);
               dc.saveItem(dil);
+              
+              //jsonMessages.add("Created " + dil.getName() + "; volume=" + Values.formatNumber(usedVolumeForExtra, 2));
             }
             
-            //jsonMessages.add("Using " + Values.formatNumber(usedQuantityForPool*1000, 2) + "+" + Values.formatNumber(usedQuantityForExtra*1000, 2) +"ng of " + Values.formatNumber(lib.getOriginalQuantity()*1000,2) + "ng from " + lib.getName()+"; molarity="+molarity);
+            //jsonMessages.add("Using " + Values.formatNumber(usedQuantityForPool*1000, 2) + "+" + Values.formatNumber(usedQuantityForExtra*1000, 2) +"ng of " + Values.formatNumber(lib.getOriginalQuantity()*1000,2) + "ng from " + lib.getName()+"; molarity="+Values.formatNumber(molarity, 2) + "(" + Values.formatNumber(molarityForPool, 2) + ")");
           }
           
@@ -387 +389 @@
           jsonMessages.add("Created '" + pool.getName() + "' from " + jsonLibs.size() + " libraries; pool molarity=" + Values.formatNumber(summedPoolMolarity / jsonLibs.size(), 2)); // conc="+Values.formatNumber(poolQuantity * 1000 / poolVolume, 2) + "ng/µl; quantity="+Values.formatNumber(poolQuantity*1000, 2)+"ng; volume="+Values.formatNumber(poolVolume, 2) + "µl");
         }
+        
         dc.commit();
       }
@@ -476 +479 @@
         Float dilQuantity = dil.getOriginalQuantity();
         //Float dilConc = (Float)Annotationtype.POOL_CONC.getAnnotationValue(dc, dil);
-        lib.setAnnotation("extraMixFactor", dilQuantity / usedQuantity);
+        lib.setAnnotation("mixFactor", (dilQuantity + usedQuantity) / usedQuantity);
       }
       
       lib.setAnnotation("dils", result.size());
-      
     }
     else
@@ -486 +488 @@
       // Calculate mix volumes, but do not correct for negative volumes 
       // due to low concentration (this will be notified in the protocols)
-      float usedVolumeForMix = TARGET_VOLUME_IN_POOL_PER_LIB * TARGET_MOLARITY_IN_POOL / molarity;
+      // Round to 1 decimal since that is the expected accuracy of pipettes
+      // Remember to use the rounded values in the calculations 
+      float usedVolumeForMix = Reggie.round(TARGET_VOLUME_IN_POOL_PER_LIB * TARGET_MOLARITY_IN_POOL / molarity, 1);
+      float mixFactor = 1.0f;
+      if (usedVolumeForMix < LIMIT_FOR_EXTRA_LARGE_MIX)
+      {
+        // Extra large mix is required if the usedVolume is small due to 
+        // difficulties to pipette the exact amount for small volumes
+        mixFactor = EXTRA_LARGE_MIX_FACTOR;
+        // Re-calculate volume to get the rounding correct
+        usedVolumeForMix = Reggie.round(mixFactor * TARGET_VOLUME_IN_POOL_PER_LIB * TARGET_MOLARITY_IN_POOL / molarity, 1) / mixFactor;
+      }
+      
       float ebVolumeForMix = TARGET_VOLUME_IN_POOL_PER_LIB - usedVolumeForMix;
       lib.setAnnotation("volume", usedVolumeForMix);
       lib.setAnnotation("eb", ebVolumeForMix);
-      // Extra large mix is required if the usedVolume is small due to 
-      // difficulties to pipette the exact amount for small volumes
-      lib.setAnnotation("extraMixFactor", usedVolumeForMix < LIMIT_FOR_EXTRA_LARGE_MIX ? EXTRA_LARGE_MIX_FACTOR : 0);
+      lib.setAnnotation("mixMolarity", molarity * usedVolumeForMix / TARGET_VOLUME_IN_POOL_PER_LIB);
+      lib.setAnnotation("mixFactor", mixFactor);
     }
   }