The MIT License Copyright (c) 2008 the RDML-consortium Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. Description of the cDNA synthesis method. Enzyme used for reverse transcription. True if RNA was DNAse treated prior cDNA synthesis. For some commercial assays the primer sequences may be unknown. This element allows to describe commercial assays. The method used to determine the cq value. Software name and version used to collect the data. Due to the high numbers of this elements names are kept short. TargetID - A reference to a target. Quantification cycle - The calculated fractional cycle where amplification was detected. Quantity - A calculated quantity based on the quantity provided with the standard samples. Excluded - Present if this entry should not be evaluated. It can contain an string with an explanation why it was excluded. Amplification data point - The single data points measured during amplification. Melting curve data point - The single data points measured in the melting analysis. End point - Result of an endpoint measurement. Background fluorescence - The measured background fluorescence. Quantification flourescence - The fluorescence corresponding to the treshold line. These elements should be used if the same description applies to many samples, targets or experiments. Due to the high numbers of this element, names are kept short. Cycle - The cycle of this data point. Temperature - The temperature in Celsius at the time of measurement. Fluorescence - The fluorescence measured. Due to the high numbers of this element, names are kept short. Temperature - The temperature in Celsius of this data point. Fluorescence - The fluorescence measured. Contact details of an experimenter. An experiment can contain several independent runs. react id within the run must be unique. Documentation references within the run types must be unique. Experimenter references within the run types must be unique. This step forms a temperature gradient on the heat block. The high temperature of the gradient in Celsius. The low temperature of the gradient in Celsius. The duration of this step in seconds. The change of the temperature from one cycle to the next: actual highTemperature = highTemperature + (temperatureChange * cycle couter) actual lowTemperature = lowTemperature + (temperatureChange * cycle couter) The change of the duration from one cycle to the next: actual duration = duration + (durationChange * cycle couter) Make a measurement and store it as meltcurve or realtime data. The temperature change from one step to the next in Celsius per second. No value means maximal change rate. A ID must be at least one character and unique. This step waits for the user to open the lid and continues after. It allows to stop the program and to wait for the user to add for example enzymes and continue the program after. The temperature of the previous step is maintained. This step allows to form a loop or to exclude some steps. It allows to jump to a certain "goto" step for "repeat" times. If the "goto" step is higher than the step of the loop, "repeat" must be "0". The step to go to forming the loop. How often the loop is repeated. The first run through the loop is counted as 0, the last loop is "repeat" - 1. The loop is run through exactly "repeat" times. Description of three prime modifications if present. Description of five prime modifications if present. This step allows to pause at a certain temperature. It is typically the last step in an amplification protocol. The temperature in Celsius to maintain during the pause. The format of the assay - This allows the software to display the data in a way which resembles the machine sample format. Due to technical improvements this list is likely to expand. Software should be able handle a "pcrFormatType" not listed here by teating them as "free format". It is required to label the "id" in "react" according to the pattern give in the enumeration. For example if "96-well plate; A1-H12" is selected a valid "id" in "react" must be in the range of "A1" to "H12". The primers used to reverse transcribe the RNA to cDNA. A quantity is always defined by its value and its unit. The unit the quantity cop - copies per microliter fold - fold change dil - dilution (10 would mean 1:10 dilution) nMol - nanomol per microliter ng - nanogram per microliter other - other unit (must be linear, no exponents or logarithms allowed) This element can be used to assign an publisher and id to the RDML file. An MD5Hash calculated over the complete file after removing all rdmlIDTypes and all whitespaces between elements. A reaction is an independent chemical reaction corresponding for example to a well in a 96 well plate, a capillary in a rotor or a droplet on the biotrophe slides. SampleID - A reference to a sample. cyc within the adp must be unique. tmp within the mdp must be unique. The ID of this reaction - The ID can be only assigned freely if "pcrFormatType" is "free format". Otherwhise it is required to label the "id" according to the pattern give in "pcrFormatType". For example if "96-well plate; A1-H12" is selected a valid "id" must be in the range of "A1" to "H12". A run is a set of reactions performed in one "run", for example one plate, a slide in a biotrophe or one rotor. Description of the instrument used to aquire the data. Description of the software used to aquire the data. Description of method used to determine the background. Description of method used to calculate the quantification cycle. The program used to aquire the data. Date and time stamp when the data was aquired. tarID within the data must be unique. A sample is a defined template solution. Dilutions of the same stock material differ in concentration and are considered different samples. A technical replicate samples should contain the same name (reactions are performed on the same material), and biological replicates should contain different names (the nucleic acids derived from the different biological replicates are not the same). True if this sample should be used as inter run calibrator Quantity - The reference quantity of this sample. This element only makes sense if the "type" is "std" or "opt". If the "type" is "std" this value should give a copy number or DNA concentration. Only the use of true numbers is valid like 1, 10, 100, 1000 or 1, 0.1, 0.01, 0.001. The use of exponents is not valid like 1, 2, 3, 4 or -1, -2, -3, -4 beause it will not be interpreted as 10E1, 10E2, 10E3, 10E4 or 10E-1, 10E-2, 10E-3. If the "type" is "opt" this value should give the DNA concentration in nanogram / microliter. Use quantUnit to indicate the unit. True if this sample was used as calibrator sample The equivalent RNA concentration in nanogram / microliter in the reaction mix. The template DNA concetration in nanogram / microliter in the reaction mix. unkn - unknown sample ntc - non template control nac - no amplification control std - standard sample opt - optical calibrator sample All the IUPAC codes : A Adenine C Cytosine G Guanine T (or U) Thymine (or Uracil) R A or G Y C or T S G or C W A or T K G or T M A or C B C or G or T D A or G or T H A or C or T V A or C or G N any base The incremental number of the step. First step should be nr = 1 and then increment each step by + 1. A target is a defined PCR reaction. PCR reactions at the same gene which differ in primer sequences are considered different samples. Amplification efficiency for the primer set is given as the exponent to the base 2. The detection limit is given in copies per microliter. Description of the dye. ref - reference gene toi - target of interest This step keeps a constant temperature on the heat block. The temperature of the step in Celsius. The duration of this step in seconds. The change of the temperature from one cycle to the next: actual temperature = temperature + (temperatureChange * cycle couter) The change of the duration from one cycle to the next: actual duration = duration + (durationChange * cycle couter) Indicates to make a measurement and store it as meltcurve or realtime data. The allowed temperature change from one step to the next in Celsius per second. No value means maximal change rate. Method used to measure quality, for example "Spectroscopy, OD 260/280". The measured value. A cycling program for PCR or to amplify cDNA. The temperature in Celsius the lid should keep during the cycling. Reference to the person who made or uses this protocol. The steps a protocol runs through to amplify DNA. This is the place to insert extensions not supported by RDML. Please use a descriptive and unique root element to avoid interference with other third party extensions. Reference to an external database, for example "genebank". The ID of the entry within the external database, for example "AJ832138". The timestamp of the creation of this file. The timestamp of the last update of this file. xRefs within the sample types must be unique. Documentation references within the sample types must be unique. xRefs within the sample types must be unique. Documentation references within the target types must be unique. step nr within the thermalCyclingConditions must be unique. Documentation references within the thermalCyclingConditions types must be unique. Experimenter references within the thermalCyclingConditions types must be unique. run IDs within the experiment types must be unique. Documentation references within the experiment types must be unique.