Sample Interactive Troubleshooting Checklist: Fill & Download for Free

I'm not too familiar with enzyme inhibition assays, but here I'll just give some common (and oft ignored) advice about how to choose controls.Learning how to set up the right kind of controls is inarguably one of the most important and basic aspects of experimental design, as you can't actually demonstrate and convince other people that your experimental results are valid and not artifacts without good controls.There are two very simple yet crucial guidelines for knowing how to decide on the correct controls:Know how everything works. And by this, I mean everything. For any protocol that use, you should knowWhat each and every step in the protocol doesWhy specific reagents are used at different stagesWhat's going on with your sample at every stepMerits and demerits of your protocolAlternative protocols or methods you can useFor any biological sample that you use, you should know things likeThe specific properties of your cells/proteins/DNA, whatever you're usingThe background behind how your cells/proteins/DNA work (you should be really familiar with this)How they may differ from other similar samplesWhether there was anything different/wrong about them before you started using themThe reason you need to know all of these things about your protocols is so that you can:Troubleshoot. Because if you know how your protocol works, then you should be able to figure out where things can go wrong. There can be a hundred different reasons an experiment can spit out errors or misleading data without anyone noticing, even when people have been particularly attentive. Now think of all the possible false results you might get if you're not paying any attention to what you're doing. Basically, before you start your experiment:Make a checklist of all the things that could possibly go wrongDesign controls that can demonstrate whether or not things actually went wrong at these placesInclude as many controls as possibleGenerally speaking, I've noticed that the really good journals have data that are supported by excellent controls, both in the main text as well as supplementary information. The not-so-nice journals have data based on somewhat sketchy controls, which often makes you want to not completely trust their data. So yeah, controls are important.How to decide on positive/negative controls:Apply the same principles when deciding what to use as positive/negative controls. What kinds of things could go wrong that could give you false positives or false negatives?Negative controls: Here you need to eliminate anything that could cause your experiments to go wrong. Perhaps the buffers you use make your samples behave in a funny way, so you need to make sure the results you get are authentic and not caused by the buffers. Perhaps you have non-specific interactions between things in your samples, perhaps there's too much variability between your actual (not control) samples; you need negative control samples to ensure that you get consistent results.Positive controls: You need these to make sure your experiment is actually working the way it should, and that the lack of results is not just due to a bad protocol or bad reagents. Perhaps your enzymes are being inactivated by something in the buffer, so use a control sample to make sure your enzymes actually work.The kind of controls you need really vary on an experiment-by-experiment basis, so the best way to figure them out is to look through good (and recent) papers in which people have previously performed similar experiments. If you still have questions, feel free to ask them here.

BasicsVariablesPrimitive Data TypesArraysSummary of VariablesQuestions and Exercises: VariablesOperatorsAssignment, Arithmetic, and Unary OperatorsEquality, Relational, and Conditional OperatorsBitwise and Bit Shift OperatorsSummary of OperatorsQuestions and Exercises: OperatorsExpressions, Statements, and BlocksQuestions and Exercises: Expressions, Statements, and BlocksControl Flow StatementsThe if-then and if-then-else StatementsThe switch StatementThe while and do-while StatementsThe for StatementBranching StatementsSummary of Control Flow StatementsQuestions and Exercises: Control Flow StatementsClasses and ObjectsClassesDeclaring ClassesDeclaring Member VariablesDefining MethodsProviding Constructors for Your ClassesPassing Information to a Method or a ConstructorObjectsCreating ObjectsUsing ObjectsMore on ClassesReturning a Value from a MethodUsing the this KeywordControlling Access to Members of a ClassUnderstanding Class MembersInitializing FieldsSummary of Creating and Using Classes and ObjectsQuestions and Exercises: ClassesQuestions and Exercises: ObjectsNested ClassesInner Class ExampleLocal ClassesAnonymous ClassesLambda ExpressionsMethod ReferencesWhen to Use Nested Classes, Local Classes, Anonymous Classes, and Lambda ExpressionsQuestions and Exercises: Nested ClassesEnum TypesQuestions and Exercises: Enum TypesAnnotationsAnnotations BasicsDeclaring an Annotation TypePredefined Annotation TypesType Annotations and Pluggable Type SystemsRepeating AnnotationsQuestions and Exercises: AnnotationsInterfaces and InheritanceInterfacesDefining an InterfaceImplementing an InterfaceUsing an Interface as a TypeEvolving InterfacesDefault MethodsSummary of InterfacesQuestions and Exercises: InterfacesInheritanceMultiple Inheritance of State, Implementation, and TypeOverriding and Hiding MethodsPolymorphismHiding FieldsUsing the Keyword superObject as a SuperclassWriting Final Classes and MethodsAbstract Methods and ClassesSummary of InheritanceQuestions and Exercises: InheritanceNumbers and StringsNumbersThe Numbers ClassesFormatting Numeric Print OutputBeyond Basic ArithmeticSummary of NumbersQuestions and Exercises: NumbersCharactersStringsConverting Between Numbers and StringsManipulating Characters in a StringComparing Strings and Portions of StringsThe StringBuilder ClassSummary of Characters and StringsAutoboxing and UnboxingQuestions and Exercises: Characters and StringsGenerics (Updated)Why Use Generics?Generic TypesRaw TypesGeneric MethodsBounded Type ParametersGeneric Methods and Bounded Type ParametersGenerics, Inheritance, and SubtypesType InferenceWildcardsUpper Bounded WildcardsUnbounded WildcardsLower Bounded WildcardsWildcards and SubtypingWildcard Capture and Helper MethodsGuidelines for Wildcard UseType ErasureErasure of Generic TypesErasure of Generic MethodsEffects of Type Erasure and Bridge MethodsNon-Reifiable TypesRestrictions on GenericsQuestions and Exercises: GenericsPackagesCreating and Using PackagesCreating a PackageNaming a PackageUsing Package MembersManaging Source and Class FilesSummary of Creating and Using PackagesQuestions and Exercises: Creating and Using PackagesTrail: Essential ClassesExceptionsWhat Is an Exception?The Catch or Specify RequirementCatching and Handling ExceptionsThe try BlockThe catch BlocksThe finally BlockThe try-with-resources StatementPutting It All TogetherSpecifying the Exceptions Thrown by a MethodHow to Throw ExceptionsChained ExceptionsCreating Exception ClassesUnchecked Exceptions — The ControversyAdvantages of ExceptionsSummaryQuestions and ExercisesBasic I/OI/O StreamsByte StreamsCharacter StreamsBuffered StreamsScanning and FormattingScanningFormattingI/O from the Command LineData StreamsObject StreamsFile I/O (Featuring NIO.2)What Is a Path? (And Other File System Facts)The Path ClassPath OperationsFile OperationsChecking a File or DirectoryDeleting a File or DirectoryCopying a File or DirectoryMoving a File or DirectoryManaging Metadata (File and File Store Attributes)Reading, Writing, and Creating FilesRandom Access FilesCreating and Reading DirectoriesLinks, Symbolic or OtherwiseWalking the File TreeFinding FilesWatching a Directory for ChangesOther Useful MethodsLegacy File I/O CodeSummaryQuestions and Exercises: Basic I/OConcurrencyProcesses and ThreadsThread ObjectsDefining and Starting a ThreadPausing Execution with SleepInterruptsJoinsThe SimpleThreads ExampleSynchronizationThread InterferenceMemory Consistency ErrorsSynchronized MethodsIntrinsic Locks and SynchronizationAtomic AccessLivenessDeadlockStarvation and LivelockGuarded BlocksImmutable ObjectsA Synchronized Class ExampleA Strategy for Defining Immutable ObjectsHigh Level Concurrency ObjectsLock ObjectsExecutorsExecutor InterfacesThread PoolsFork/JoinConcurrent CollectionsAtomic VariablesConcurrent Random NumbersFor Further ReadingQuestions and Exercises: ConcurrencyThe Platform EnvironmentConfiguration UtilitiesPropertiesCommand-Line ArgumentsEnvironment VariablesOther Configuration UtilitiesSystem UtilitiesCommand-Line I/O ObjectsSystem PropertiesThe Security ManagerMiscellaneous Methods in SystemPATH and CLASSPATHQuestions and Exercises: The Platform EnvironmentRegular ExpressionsIntroductionTest HarnessString LiteralsCharacter ClassesPredefined Character ClassesQuantifiersCapturing GroupsBoundary MatchersMethods of the Pattern ClassMethods of the Matcher ClassMethods of the PatternSyntaxException ClassUnicode SupportAdditional ResourcesQuestions and Exercises: Regular ExpressionsTrail: DeploymentJava AppletsGetting Started With AppletsDefining an Applet SubclassMethods for MilestonesLife Cycle of an AppletApplet's Execution EnvironmentDeveloping an AppletDeploying an AppletDeploying With the Applet TagDoing More With AppletsFinding and Loading Data FilesDefining and Using Applet ParametersDisplaying Short Status StringsDisplaying Documents in the BrowserInvoking JavaScript Code From an AppletInvoking Applet Methods From JavaScript CodeHandling Initialization Status With Event HandlersManipulating DOM of Applet's Web PageDisplaying a Customized Loading Progress IndicatorWriting Diagnostics to Standard Output and Error StreamsDeveloping Draggable AppletsCommunicating With Other AppletsWorking With a Server-Side ApplicationNetwork Client Applet ExampleWhat Applets Can and Cannot DoSolving Common Applet ProblemsQuestions and Exercises: AppletsJava Web StartDeveloping a Java Web Start ApplicationRetrieving ResourcesDeploying a Java Web Start ApplicationSetting Up a Web ServerDisplaying a Customized Loading Progress IndicatorRunning a Java Web Start ApplicationJava Web Start and SecurityCommon Java Web Start ProblemsQuestions and Exercises: Java Web StartDoing More With Java Rich Internet ApplicationsSetting Trusted Arguments and Secure PropertiesSystem PropertiesJNLP APIAccessing the Client Using JNLP APICookiesAccessing CookiesCustomizing the Loading ExperienceSecurity in Rich Internet ApplicationsGuidelines for Securing Rich Internet ApplicationsQuestions and Exercises: Doing More With Rich Internet ApplicationsDeployment In-DepthUser Acceptance of RIAsDeployment ToolkitDeploying an AppletCustomizing the Loading ScreenEmbedding JNLP File in Applet TagDeploying a Java Web Start ApplicationChanging the Launch ButtonDeploying Without CodebaseChecking the Client JRE Software VersionJava Network Launch ProtocolStructure of the JNLP FileDeployment Best PracticesReducing the Download TimeAvoiding Unnecessary Update ChecksEnsuring the Presence of the JRE SoftwareQuestions and Exercises: Deployment In-DepthDeploying Self-Contained ApplicationsPre-Requisites for Packaging Self-Contained ApplicationsConverting an Existing ApplicationUsing File AssociationsAdding an External LibraryProviding a Default ArgumentUsing a Common Build File for All PlatformsUsing Multiple Entry PointsQuestions and Exercises: Self-Contained ApplicationsPackaging Programs in JAR FilesUsing JAR Files: The BasicsCreating a JAR FileViewing the Contents of a JAR FileExtracting the Contents of a JAR FileUpdating a JAR FileRunning JAR-Packaged SoftwareWorking with Manifest Files: The BasicsUnderstanding the Default ManifestModifying a Manifest FileSetting an Application's Entry PointAdding Classes to the JAR File's ClasspathSetting Package Version InformationSealing Packages within a JAR FileEnhancing Security with Manifest AttributesSigning and Verifying JAR FilesUnderstanding Signing and VerificationSigning JAR FilesVerifying Signed JAR FilesUsing JAR-related APIsThe JarClassLoader ClassThe JarRunner ClassQuestions and Exercises: JARTrail: Creating a GUI With JFC/SwingGetting Started with SwingAbout the JFC and SwingCompiling and Running Swing ProgramsLearning Swing with the NetBeans IDESetting up the CelsiusConverter ProjectNetBeans IDE BasicsCreating the CelsiusConverter GUIAdjusting the CelsiusConverter GUIAdding the Application LogicQuestions and Exercises: Learning Swing with the NetBeans IDEUsing Swing ComponentsUsing Top-Level ContainersThe JComponent ClassUsing Text ComponentsText Component FeaturesThe Text Component APIHow to Use Various ComponentsHow to Make AppletsHow to Use Buttons, Check Boxes, and Radio ButtonsHow to Use the ButtonGroup ComponentHow to Use Color ChoosersHow to Use Combo BoxesHow to Make DialogsHow to Use Editor Panes and Text PanesHow to Use File ChoosersHow to Use Formatted Text FieldsHow to Make Frames (Main Windows)How to Use Internal FramesHow to Use LabelsHow to Use Layered PanesHow to Use ListsHow to Use MenusHow to Use PanelsHow to Use Password FieldsHow to Use Progress BarsHow to Use Root PanesHow to Use Scroll PanesHow to Use SeparatorsHow to Use SlidersHow to Use SpinnersHow to Use Split PanesHow to Use Tabbed PanesHow to Use TablesHow to Use Text AreasHow to Use Text FieldsHow to Use Tool BarsHow to Use Tool TipsHow to Use TreesHow to Use HTML in Swing ComponentsHow to Use ModelsHow to Use IconsHow to Use BordersSolving Common Component ProblemsQuestions and Exercises: Using Swing ComponentsConcurrency in SwingInitial ThreadsThe Event Dispatch ThreadWorker Threads and SwingWorkerSimple Background TasksTasks that Have Interim ResultsCanceling Background TasksBound Properties and Status MethodsQuestions and Exercises: Concurrency in SwingUsing Other Swing FeaturesHow to Integrate with the Desktop ClassHow to Create Translucent and Shaped WindowsHow to Decorate Components with the JLayer ClassHow to Use ActionsHow to Use Swing TimersHow to Support Assistive TechnologiesHow to Use the Focus SubsystemHow to Use Key BindingsHow to Use Modality in DialogsHow to Print TablesHow to Print TextHow to Create a Splash ScreenHow to Use the System TraySolving Common Problems Using Other Swing FeaturesLaying Out Components Within a ContainerA Visual Guide to Layout ManagersUsing Layout ManagersHow Layout Management WorksHow to Use Various Layout ManagersHow to Use BorderLayoutHow to Use BoxLayoutHow to Use CardLayoutHow to Use FlowLayoutHow to Use GridBagLayoutHow to Use GridLayoutHow to Use GroupLayoutA GroupLayout ExampleHow to Use SpringLayoutCreating a Custom Layout ManagerDoing Without a Layout Manager (Absolute Positioning)Solving Common Layout ProblemsQuestions and Exercises: Laying Out Components within a ContainerModifying the Look and FeelHow to Set the Look and FeelThe Synth Look and FeelA Synth ExampleNimbus Look and FeelChanging the Look of NimbusResizing a ComponentChanging the Color ThemeFor More InformationDrag and Drop and Data TransferIntroduction to DnDDefault DnD SupportDemo - BasicDnDTransferHandler ClassExport MethodsImport MethodsTransferSupport ClassSetting the Drop ModeDemo - DropDemoChoosing the Drop ActionDemo - ChooseDropActionShowing the Drop LocationLocation Sensitive DropDemo - LocationSensitiveDemoEmpty Table DropDrop Location RenderingTop-Level DropAdding Cut, Copy and Paste (CCP)CCP in a Text ComponentCCP in a non-Text ComponentUsing and Creating a DataFlavorPutting it All Together - DnD and CCPFurther InformationSolving Common Data Transfer ProblemsWriting Event ListenersIntroduction to Event ListenersGeneral Information about Writing Event ListenersListeners Supported by Swing ComponentsImplementing Listeners for Commonly Handled EventsHow to Write an Action ListenerHow to Write a Caret ListenerHow to Write a Change ListenerHow to Write a Component ListenerHow to Write a Container ListenerHow to Write a Document ListenerHow to Write a Focus ListenerHow to Write an Internal Frame ListenerHow to Write an Item ListenerHow to Write a Key ListenerHow to Write a List Data ListenerHow to Write a List Selection ListenerHow to Write a Mouse ListenerHow to Write a Mouse-Motion ListenerHow to Write a Mouse-Wheel ListenerHow to Write a Property Change ListenerHow to Write a Table Model ListenerHow to Write a Tree Expansion ListenerHow to Write a Tree Model ListenerHow to Write a Tree Selection ListenerHow to Write a Tree-Will-Expand ListenerHow to Write an Undoable Edit ListenerHow to Write Window ListenersListener API TableSolving Common Event-Handling ProblemsQuestions and Exercises: Writing Event ListenersPerforming Custom PaintingCreating the Demo Application (Step 1)Creating the Demo Application (Step 2)Creating the Demo Application (Step 3)Refining the DesignA Closer Look at the Paint MechanismSummarySolving Common Painting ProblemsQuestions and Exercises: Performing Custom PaintingTrail: CollectionsIntroduction to CollectionsInterfacesThe Collection InterfaceThe Set InterfaceThe List InterfaceThe Queue InterfaceThe Deque InterfaceThe Map InterfaceObject OrderingThe SortedSet InterfaceThe SortedMap InterfaceSummary of InterfacesQuestions and Exercises: InterfacesAggregate OperationsReductionParallelismQuestions and Exercises: Aggregate OperationsImplementationsSet ImplementationsList ImplementationsMap ImplementationsQueue ImplementationsDeque ImplementationsWrapper ImplementationsConvenience ImplementationsSummary of ImplementationsQuestions and Exercises: ImplementationsAlgorithmsCustom Collection ImplementationsInteroperabilityCompatibilityAPI DesignTrail: Date TimeDate-Time OverviewDate-Time Design PrinciplesThe Date-Time PackagesMethod Naming ConventionsStandard CalendarOverviewDayOfWeek and Month EnumsDate ClassesDate and Time ClassesTime Zone and Offset ClassesInstant ClassParsing and FormattingThe Temporal PackageTemporal AdjusterTemporal QueryPeriod and DurationClockNon-ISO Date ConversionLegacy Date-Time CodeSummaryQuestions and Exercises: Date-Time APITrail: InternationalizationIntroductionA Quick ExampleBefore InternationalizationAfter InternationalizationRunning the Sample ProgramInternationalizing the Sample ProgramChecklistSetting the LocaleCreating a LocaleBCP 47 ExtensionsIdentifying Available LocalesLanguage Tag Filtering and LookupThe Scope of a LocaleLocale-Sensitive Services SPIIsolating Locale-Specific DataAbout the ResourceBundle ClassPreparing to Use a ResourceBundleBacking a ResourceBundle with Properties FilesUsing a ListResourceBundleCustomizing Resource Bundle LoadingFormattingNumbers and CurrenciesUsing Predefined FormatsCustomizing FormatsDates and TimesUsing Predefined FormatsCustomizing FormatsChanging Date Format SymbolsMessagesDealing with Compound MessagesHandling PluralsWorking with TextChecking Character PropertiesComparing StringsPerforming Locale-Independent ComparisonsCustomizing Collation RulesImproving Collation PerformanceUnicodeTerminologySupplementary Characters as SurrogatesCharacter and String APIsSample UsageDesign ConsiderationsMore InformationDetecting Text BoundariesAbout the BreakIterator ClassCharacter BoundariesWord BoundariesSentence BoundariesLine BoundariesConverting Latin Digits to Other Unicode DigitsConverting Non-Unicode TextByte Encodings and StringsCharacter and Byte StreamsNormalizing TextWorking with Bidirectional Text with the JTextComponent ClassInternationalization of Network ResourcesInternationalized Domain NameService Providers for InternationalizationInstalling a Custom Resource Bundle as an ExtensionTrail: 2D GraphicsOverview of the Java 2D API ConceptsCoordinatesJava 2D RenderingGeometric PrimitivesTextImagesPrintingGetting Started with GraphicsWorking with GeometryDrawing Geometric PrimitivesDrawing Arbitrary ShapesStroking and Filling Graphics PrimitivesWorking with Text APIsFont ConceptsText Layout ConceptsPhysical and Logical FontsMeasuring TextAdvanced Text DisplayDisplaying Antialiased Text by Using Rendering HintsUsing Text Attributes to Style TextDrawing Multiple Lines of TextWorking with Bidirectional TextWorking with ImagesReading/Loading an ImageDrawing an ImageCreating and Drawing to an ImageWriting/Saving an ImagePrintingA Basic Printing ProgramUsing Print Setup DialogsPrinting a Multiple Page DocumentWorking with Print Services and AttributesPrinting the Contents of a User InterfacePrinting Support in Swing ComponentsAdvanced Topics in Java2DTransforming Shapes, Text, and ImagesClipping the Drawing RegionCompositing GraphicsControlling Rendering QualityConstructing Complex Shapes from Geometry PrimitivesSupporting User InteractionTrail: SoundOverview of the Sampled PackageAccessing Audio System ResourcesPlaying Back AudioCapturing AudioProcessing Audio with ControlsUsing Files and Format ConvertersOverview of the MIDI PackageAccessing MIDI System ResourcesTransmitting and Receiving MIDI MessagesIntroduction to SequencersUsing Sequencer MethodsUsing Advanced Sequencer FeaturesSynthesizing SoundIntroduction to the Service Provider InterfacesProviding Sampled-Audio ServicesProviding MIDI ServicesTrail: JavaBeans(TM)Quick StartCreating a ProjectA Button is a BeanWiring the ApplicationUsing a Third-Party BeanWriting JavaBeans ComponentsPropertiesMethodsEventsUsing a BeanInfoAdvanced JavaBeans TopicsBean PersistenceLong Term PersistenceBean CustomizationTrail: JDBC(TM) Database AccessJDBC IntroductionJDBC ArchitectureA Relational Database OverviewJDBC BasicsGetting StartedProcessing SQL Statements with JDBCEstablishing a ConnectionConnecting with DataSource ObjectsHandling SQLExceptionsSetting Up TablesRetrieving and Modifying Values from Result SetsUsing Prepared StatementsUsing TransactionsUsing RowSet ObjectsUsing JdbcRowSet ObjectsUsing CachedRowSetObjectsUsing JoinRowSet ObjectsUsing FilteredRowSet ObjectsUsing WebRowSet ObjectsUsing Advanced Data TypesUsing Large ObjectsUsing SQLXML ObjectsUsing Array ObjectsUsing DISTINCT Data TypeUsing Structured ObjectsUsing Customized Type MappingsUsing Datalink ObjectsUsing RowId ObjectsUsing Stored ProceduresUsing JDBC with GUI APITrail: Java Management Extensions (JMX)Overview of the JMX TechnologyWhy Use the JMX Technology?Architecture of the JMX TechnologyMonitoring and Management of the Java Virtual MachineIntroducing MBeansStandard MBeansMXBeansNotificationsRemote ManagementExposing a Resource for Remote Management By JConsoleCreating a Custom JMX ClientTrail: Java API for XML Processing (JAXP)Introduction to JAXPOverview of the PackagesSimple API for XML APIsDocument Object Model APIsExtensible Stylesheet Language Transformations APIsStreaming API for XML APIsFinding the JAXP Sample ProgramsWhere Do You Go From Here?Simple API for XMLWhen to Use SAXParsing an XML File Using SAXImplementing SAX ValidationHandling Lexical EventsUsing the DTDHandler and EntityResolverFurther InformationDocument Object ModelWhen to Use DOMReading XML Data into a DOMValidating with XML SchemaFurther InformationExtensible Stylesheet Language TransformationsIntroducing XSL, XSLT, and XPathHow XPath WorksWriting Out a DOM as an XML FileGenerating XML from an Arbitrary Data StructureTransforming XML Data with XSLTStreaming API for XMLWhy StAX?StAX APIUsing StAXOracle's Streaming XML Parser ImplementationExample CodeFurther InformationJAXP 1.5 and New PropertiesBackgroundExternal ResourcesNew PropertiesScope and OrderRelationship with the SecurityManagerProperty Settings in the JDKUsing the PropertiesError HandlingStAXConclusionReferencesProcessing LimitsProcessing Limit DefinitionsScope and OrderUsing the LimitsError HandlingStAXSamplesTrail: RMIAn Overview of RMI ApplicationsWriting an RMI ServerDesigning a Remote InterfaceImplementing a Remote InterfaceCreating a Client ProgramCompiling and Running the ExampleCompiling the Example ProgramsRunning the Example ProgramsTrail: Security Features in Java SESecurity Features OverviewCreating a Policy FileSet up a Policy File to Grant the Required PermissionStart Policy ToolGrant the Required PermissionSave the Policy FileQuick Tour of Controlling ApplicationsObserve Application FreedomSee How to Restrict ApplicationsSet up the Policy File to Grant the Required PermissionsOpen the Policy FileGrant the Required PermissionsSave the Policy FileSee the Policy File EffectsAPI and Tools Use for Secure Code and File ExchangesSigning Code and Granting It PermissionsSteps for the Code SignerDownload and Try the Sample ApplicationCreate a JAR File Containing the Class FileGenerate KeysSign the JAR FileExport the Public Key CertificateSteps for the Code ReceiverObserve the Restricted ApplicationImport the Certificate as a Trusted CertificateSet Up a Policy File to Grant the Required PermissionStart Policy ToolSpecify the KeystoreAdd a Policy Entry with a SignedBy AliasSave the Policy FileSee the Policy File EffectsExchanging FilesSteps for the Contract SenderCreate a JAR File Containing the ContractGenerate KeysSign the JAR FileExport the Public Key CertificateSteps for the Contract ReceiverImport the Certificate as a Trusted CertificateVerify the JAR File SignatureGenerating and Verifying SignaturesGenerating a Digital SignaturePrepare Initial Program StructureGenerate Public and Private KeysSign the DataSave the Signature and the Public Key in FilesCompile and Run the ProgramVerifying a Digital SignaturePrepare Initial Program StructureInput and Convert the Encoded Public Key BytesInput the Signature BytesVerify the SignatureCompile and Run the ProgramWeaknesses and AlternativesImplementing Your Own PermissionExampleGameThe HighScore ClassThe HighScorePermission ClassA Sample Policy FilePutting It All TogetherSteps for the HighScore Developer (Chris)Steps for the ExampleGame Developer (Terry)Steps for a User Running ExampleGame (Kim)Trail: The Extension MechanismCreating and Using ExtensionsInstalled ExtensionsDownload ExtensionsUnderstanding Extension Class LoadingCreating Extensible ApplicationsMaking Extensions SecureSetting Privileges for ExtensionsSealing Packages in ExtensionsTrail: The Reflection APIClassesRetrieving Class ObjectsExamining Class Modifiers and TypesDiscovering Class MembersTroubleshootingMembersFieldsObtaining Field TypesRetrieving and Parsing Field ModifiersGetting and Setting Field ValuesTroubleshootingMethodsObtaining Method Type InformationObtaining Names of Method ParametersRetrieving and Parsing Method ModifiersInvoking MethodsTroubleshootingConstructorsFinding ConstructorsRetrieving and Parsing Constructor ModifiersCreating New Class InstancesTroubleshootingArrays and Enumerated TypesArraysIdentifying Array TypesCreating New ArraysGetting and Setting Arrays and Their ComponentsTroubleshootingEnumerated TypesExamining EnumsGetting and Setting Fields with Enum TypesTroubleshootingTrail: Custom NetworkingOverview of NetworkingWhat You May Already Know About Networking in JavaNetworking BasicsWorking with URLsWhat Is a URL?Creating a URLParsing a URLReading Directly from a URLConnecting to a URLReading from and Writing to a URLConnectionAll About SocketsWhat Is a Socket?Reading from and Writing to a SocketWriting the Server Side of a SocketAll About DatagramsWhat Is a Datagram?Writing a Datagram Client and ServerBroadcasting to Multiple RecipientsProgrammatic Access to Network ParametersWhat Is a Network Interface?Retrieving Network InterfacesListing Network Interface AddressesNetwork Interface ParametersWorking With CookiesHTTP State Management With CookiesCookieHandler Callback MechanismDefault CookieManagerCustom CookieManagerTrail: BonusGenericsIntroductionDefining Simple GenericsGenerics and SubtypingWildcardsGeneric MethodsInteroperating with Legacy CodeThe Fine PrintClass Literals as Runtime-Type TokensMore Fun with WildcardsConverting Legacy Code to Use GenericsAcknowledgementsfind more here…Source : The Really Big Index