{"__v":69,"_id":"560c175ae6112f2300b8d9a1","api":{"auth":"never","params":[],"results":{"codes":[]},"settings":"","url":""},"body":"[block:html]\n{\n  \"html\": \"<style>\\n  .welcome {\\n    background-color: #3b4a59;\\n    color: white;\\n    font-size: 16px;\\n    text-align: center;\\n    padding: 60px;\\n    font-family: \\\"Source Sans Pro\\\";\\n  }\\n \\t\\n  .link {\\n    color: #ffc40c;\\n  }\\n  .link::hover {\\n    text-decoration: underline;\\n    color: white;\\n  }\\n</style>\\n<div class=\\\"welcome\\\">\\n  <h3>Welcome to the Transcriptic Developer Center!</h3>\\n\\n<p>Here you'll find comprehensive documentation to help you start working with Transcriptic as quickly as possible.  Read below for a quick overview or use the navigation on the left or the search bar above to explore other topics.</p>\\n\\n<p>If you can't find the answer to your question here, please <a class=\\\"link\\\" href=\\\"http://forum.transcriptic.com\\\">visit the community forum!</a></p>\\n</div>\"\n}\n[/block]\nTranscriptic allows you to run automated experiments remotely by launching [runs](doc:what-is-a-run) from our library of pre-defined and validated [protocols](doc:background) using your own samples.\n\n\nThis document will cover the basics of getting started with Transcriptic, including:\n   - [How to send us your samples and populate your inventory](https://developers.transcriptic.com/docs/getting-started#send-us-your-samples)\n   - [Lauching one of our standard validated protocols](https://developers.transcriptic.com/docs/getting-started#launching-a-standard-protocol)\n   - [Custom protocol implementation](https://developers.transcriptic.com/docs/getting-started#custom-protocol-implementation)\n   - [Developing your own protocol](https://developers.transcriptic.com/docs/getting-started#developing-your-own-protocols)\n[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"Send Us Your Samples\"\n}\n[/block]\n\n[block:callout]\n{\n  \"type\": \"danger\",\n  \"title\": \"Prohibited materials\",\n  \"body\": \"Transcriptic prohibits the use without prior approval of a list of material classes. Please see the documentation on [Hazardous Materials](doc:hazardous-materials).\"\n}\n[/block]\nBefore you can launch any protocol, you must arrange for Transcriptic to have your samples on hand.  Samples you wish to analyze that exist in your lab should be transferred into Transcriptic tubes or 96-well plates that you receive in an Intake Kit.  Commercial reagents can also be reformatted into Transcriptic-compatible containers and sent to us.  You are responsible for shipping your reagents back to Transcriptic with packing material sufficient to keep your samples at the desired temperature.  \n[block:callout]\n{\n  \"type\": \"warning\",\n  \"title\": \"Shipping Commercial Reagents to Transcriptic\",\n  \"body\": \"Some commercial reagents can be shipped directly to Transcriptic from the vendor. We will accept liquid reagents in microtubes or microplates. These reagents will be reformatted into Transcriptic compatible containers upon arrival. This process will incur a $50 intake fee per 96-pcr plate or 12 1.5mL tubes.  You will still need to populate your inventory (see below) so that we can expect the shipment and know how to reformat the reagents received into Transcriptic-compatible containers.\"\n}\n[/block]\n## Step 1: Request an Intake Kit\n\nTo request an intake kit containing plates and tubes compatible with Transcriptic's automation, navigate to your Inventory tab, click on Intake Kits, and then click the Request Intake Kit Button.  Make sure you've entered a payment method before you continue. \n\n[block:embed]\n{\n  \"html\": \"<iframe class=\\\"embedly-embed\\\" src=\\\"//cdn.embedly.com/widgets/media.html?src=https%3A%2F%2Fwww.youtube.com%2Fembed%2FlOENIPftv-Q%3Ffeature%3Doembed&url=https%3A%2F%2Fwww.youtube.com%2Fwatch%3Fv%3DlOENIPftv-Q&image=https%3A%2F%2Fi.ytimg.com%2Fvi%2FlOENIPftv-Q%2Fhqdefault.jpg&key=02466f963b9b4bb8845a05b53d3235d7&type=text%2Fhtml&schema=youtube\\\" width=\\\"854\\\" height=\\\"480\\\" scrolling=\\\"no\\\" frameborder=\\\"0\\\" allowfullscreen></iframe>\",\n  \"url\": \"https://www.youtube.com/watch?v=lOENIPftv-Q\",\n  \"title\": \"How to request a Sample Intake Kit on Transcriptic\",\n  \"favicon\": \"https://s.ytimg.com/yts/img/favicon-vflz7uhzw.ico\",\n  \"image\": \"https://i.ytimg.com/vi/lOENIPftv-Q/hqdefault.jpg\"\n}\n[/block]\nOnce you've filled in your shipping address and requested a kit, it will show up under the \"In Transit to You\" section.  \n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/gnCWXazNQpOlnQgTW0hc_Fullscreen_9_30_15__10_46_AM.png\",\n        \"Fullscreen_9_30_15__10_46_AM.png\",\n        \"660\",\n        \"199\",\n        \"#a54b33\",\n        \"\"\n      ]\n    }\n  ]\n}\n[/block]\n## Step 2:  Populate Your Inventory\n\nOnce you've requested a kit, you can populate your inventory with the samples you plan to send us by navigating to the Samples tab and clicking the \"Add New Samples\" button.  From here, you can specify the names and volumes of the samples you'll be sending to us, and what container type they're in.    \n\nWhen filling out the sample intake form, the storage field is required. The available storage environments are the same ones listed in the [Containers](doc:containers) section. This location will also be the destination of that container after runs unless otherwise specified in a protocol.\n\nAfter you've entered your samples, they will be visible in your inventory and useable within protocols, however, runs will notify you that they are \"awaiting shipment\" and won't be executed until the samples are received.  \n[block:html]\n{\n  \"html\": \"<div>\\n  <video style=\\\"max-width: 100%\\\" controls>\\n  \\t<source src=\\\"//static.transcriptic.com/screencasts/populate_inventory.webm\\\" type=\\\"video/webm; codecs=vp8\\\">\\n\\t  <source src=\\\"//static.transcriptic.com/screencasts/populate_inventory.mp4\\\" type=\\\"video/mp4; codecs=avc1.64001f\\\">\\n\\t</video>\\n</div>\"\n}\n[/block]\n\n## Step 3: Mail Us Your Samples\n\nEach shipment is associated with a four letter intake code, which should be written on the packaging in which you ship us your samples. In addition, each sample (individual tube or plate) has its own 3-letter code which should be written on the container itself. If these codes aren't included, we won't be able to properly insert your samples in inventory and track them. \n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/YDFRso9ORiCrNQqo8Vot_Transcriptic_Shipment.png\",\n        \"Transcriptic_Shipment.png\",\n        \"860\",\n        \"977\",\n        \"#a0145f\",\n        \"\"\n      ]\n    }\n  ]\n}\n[/block]\n\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/fsOXOgjTRy9oyjpeUHFn_Tracking_Number.png\",\n        \"Tracking_Number.png\",\n        \"775\",\n        \"388\",\n        \"#ca1358\",\n        \"\"\n      ],\n      \"caption\": \"For expedited shipping, a tracking number can be entered on the Intake Kits page of your inventory after your samples have been shipped.\"\n    }\n  ]\n}\n[/block]\n\n[block:callout]\n{\n  \"type\": \"info\",\n  \"title\": \"Transcriptic Plates and Tubes\",\n  \"body\": \"Only the provided tubes and plates can be used with our platform. Please [contact us](mailto:support:::at:::transcriptic.com) if you have samples that cannot conform to the containers currently provided with the intake kit.\\n\\nPlease do not attach anything to Transcriptic containers. Sticky labels can interfere with the sample in take process. If you need to label your containers please write on the side of them with a permanent marker. \\n\\nIf you choose to submit your samples in your own containers or send reagents to Transcriptic from a vendor directly, you will be charged an intake fee of $50 per 96 well plate or $50 per 12 tube shipment.\"\n}\n[/block]\n\n[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"Launching a Standard Protocol\"\n}\n[/block]\n\nTo launch a standard protocol, navigate to one of your existing projects (or create a new one) and click on \"Launch a Run\" in the upper right corner.  If this is your first run in a project, you can also click the \"Browse All Protocols\" button.  On the dialog that comes up, select the protocol you wish to run. \n\nThe next screen will present you with parameters you can use to customize your protocol.  Any field that requires a Container, Aliquots or Aliquot will bring up the inventory browser, from which you can choose the appropriate object from your inventory.  \n\nOnce you're satisfied with your parameters, click \"Next\".  If the protocol is valid, the next screen will show you an overview of your protocol with the parameters and samples you chose.  You can click on each instruction card to see details about what the [Workcell](https://transcriptic.com/workcells) will be doing.   If everything looks ok, click \"Submit\".\n[block:callout]\n{\n  \"type\": \"warning\",\n  \"title\": \"Protocol Pricing\",\n  \"body\": \"Most protocols are priced on a per-reaction basis.\"\n}\n[/block]\nCongratulations! Your run is now in the queue and will begin execution shortly.  You'll get an email when the run begins and when it's completed.  If your run generated analytical data, it will be viewable under the Results tab. \n\nSee the whole process in action below:\n[block:html]\n{\n  \"html\": \"<div>\\n  <video style=\\\"max-width: 100%\\\" controls>\\n  \\t<source src=\\\"//static.transcriptic.com/screencasts/launch_run.webm\\\" type=\\\"video/webm; codecs=vp8\\\">\\n\\t  <source src=\\\"//static.transcriptic.com/screencasts/launch_run.mp4\\\" type=\\\"video/mp4; codecs=avc1.64001f\\\">\\n\\t</video>\\n</div>\"\n}\n[/block]\n\n[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"Custom Protocol Implementation\"\n}\n[/block]\nIf none of the [standard protocols](https://developers.transcriptic.com/v1.0/docs/getting-started#launching-a-standard-protocol) available are sufficient for the experiment you'd like to automate, never fear! We have an experienced team of application scientists that can help you implement a custom protocol.\n\nSend us an email at [sales@transcriptic.com](mailto:sales@transcriptic.com) with an outline of the protocol you'd like implemented and we will get back to you with specifics.\n[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"Developing Your Own Protocols\"\n}\n[/block]\nThere are two components to development at Transcriptic.  \n\nYou can develop on the individual protocol level and submit runs [through the command-line](doc:getting-started-with-the-cli).  It is suggested that you get your feet wet by first reading up on [Autoprotocol](http://autoprotocol.org), an open-source data standard Transcriptic created to document protocols in a format both humans and our workcells understand. Then, you can browse the [About Autoprotocol](doc:autoprotocol) section to read more about the tools we and others have created to make encoding protocols in Autoprotocol easier.\n\nYou can also [create a package](doc:what-is-a-package), or a custom user interface for your protocol or group of protocols (like the standard validated protocols shown above).  Creating a package is useful for repeatedly launching the same protocol over and over with different samples and/or parameters.  Check out the [Package Creation Quickstart](doc:package-creation-quickstart) for more information.\n\nThere is documentation available [here](http://autoprotocol-python.transcriptic.com/) and [here](http://autoprotocol-utilities.transcriptic.com/) .If you get stuck, a wonderful community of developers is available to help you over in [Our Community](http://forum.transcriptic.com).  \n[block:callout]\n{\n  \"type\": \"warning\",\n  \"title\": \"Developer Disclaimer\",\n  \"body\": \"By developing and submitting your own protocols without consulting Transcriptic for code review and protocol validation, you assume responsibility for any troubleshooting required to optimize your protocol for Transcriptic’s automated Workcells.   It is highly recommended that you at least read through our [Liquid Handling Design Rules](doc:liquid-handling-guide) and [How to Write a New Protocol](doc:how-to-write-a-new-protocol) sections within this documentation before you begin development.\"\n}\n[/block]","category":"54e90194c8e0c00d007ac061","createdAt":"2015-09-30T17:09:46.749Z","excerpt":"","githubsync":"","hidden":false,"isReference":false,"link_external":false,"link_url":"","order":0,"parentDoc":null,"project":"5476bf0f817e8d080031f988","slug":"getting-started","sync_unique":"","title":"Getting Started","type":"basic","updates":["5726669e87539a0e00062ad7"],"user":"54c096f492501c0d000b38a7","version":"5476bf10817e8d080031f98b","childrenPages":[]}
[block:html] { "html": "<style>\n .welcome {\n background-color: #3b4a59;\n color: white;\n font-size: 16px;\n text-align: center;\n padding: 60px;\n font-family: \"Source Sans Pro\";\n }\n \t\n .link {\n color: #ffc40c;\n }\n .link::hover {\n text-decoration: underline;\n color: white;\n }\n</style>\n<div class=\"welcome\">\n <h3>Welcome to the Transcriptic Developer Center!</h3>\n\n<p>Here you'll find comprehensive documentation to help you start working with Transcriptic as quickly as possible. Read below for a quick overview or use the navigation on the left or the search bar above to explore other topics.</p>\n\n<p>If you can't find the answer to your question here, please <a class=\"link\" href=\"http://forum.transcriptic.com\">visit the community forum!</a></p>\n</div>" } [/block] Transcriptic allows you to run automated experiments remotely by launching [runs](doc:what-is-a-run) from our library of pre-defined and validated [protocols](doc:background) using your own samples. This document will cover the basics of getting started with Transcriptic, including: - [How to send us your samples and populate your inventory](https://developers.transcriptic.com/docs/getting-started#send-us-your-samples) - [Lauching one of our standard validated protocols](https://developers.transcriptic.com/docs/getting-started#launching-a-standard-protocol) - [Custom protocol implementation](https://developers.transcriptic.com/docs/getting-started#custom-protocol-implementation) - [Developing your own protocol](https://developers.transcriptic.com/docs/getting-started#developing-your-own-protocols) [block:api-header] { "type": "basic", "title": "Send Us Your Samples" } [/block] [block:callout] { "type": "danger", "title": "Prohibited materials", "body": "Transcriptic prohibits the use without prior approval of a list of material classes. Please see the documentation on [Hazardous Materials](doc:hazardous-materials)." } [/block] Before you can launch any protocol, you must arrange for Transcriptic to have your samples on hand. Samples you wish to analyze that exist in your lab should be transferred into Transcriptic tubes or 96-well plates that you receive in an Intake Kit. Commercial reagents can also be reformatted into Transcriptic-compatible containers and sent to us. You are responsible for shipping your reagents back to Transcriptic with packing material sufficient to keep your samples at the desired temperature. [block:callout] { "type": "warning", "title": "Shipping Commercial Reagents to Transcriptic", "body": "Some commercial reagents can be shipped directly to Transcriptic from the vendor. We will accept liquid reagents in microtubes or microplates. These reagents will be reformatted into Transcriptic compatible containers upon arrival. This process will incur a $50 intake fee per 96-pcr plate or 12 1.5mL tubes. You will still need to populate your inventory (see below) so that we can expect the shipment and know how to reformat the reagents received into Transcriptic-compatible containers." } [/block] ## Step 1: Request an Intake Kit To request an intake kit containing plates and tubes compatible with Transcriptic's automation, navigate to your Inventory tab, click on Intake Kits, and then click the Request Intake Kit Button. Make sure you've entered a payment method before you continue. [block:embed] { "html": "<iframe class=\"embedly-embed\" src=\"//cdn.embedly.com/widgets/media.html?src=https%3A%2F%2Fwww.youtube.com%2Fembed%2FlOENIPftv-Q%3Ffeature%3Doembed&url=https%3A%2F%2Fwww.youtube.com%2Fwatch%3Fv%3DlOENIPftv-Q&image=https%3A%2F%2Fi.ytimg.com%2Fvi%2FlOENIPftv-Q%2Fhqdefault.jpg&key=02466f963b9b4bb8845a05b53d3235d7&type=text%2Fhtml&schema=youtube\" width=\"854\" height=\"480\" scrolling=\"no\" frameborder=\"0\" allowfullscreen></iframe>", "url": "https://www.youtube.com/watch?v=lOENIPftv-Q", "title": "How to request a Sample Intake Kit on Transcriptic", "favicon": "https://s.ytimg.com/yts/img/favicon-vflz7uhzw.ico", "image": "https://i.ytimg.com/vi/lOENIPftv-Q/hqdefault.jpg" } [/block] Once you've filled in your shipping address and requested a kit, it will show up under the "In Transit to You" section. [block:image] { "images": [ { "image": [ "https://files.readme.io/gnCWXazNQpOlnQgTW0hc_Fullscreen_9_30_15__10_46_AM.png", "Fullscreen_9_30_15__10_46_AM.png", "660", "199", "#a54b33", "" ] } ] } [/block] ## Step 2: Populate Your Inventory Once you've requested a kit, you can populate your inventory with the samples you plan to send us by navigating to the Samples tab and clicking the "Add New Samples" button. From here, you can specify the names and volumes of the samples you'll be sending to us, and what container type they're in. When filling out the sample intake form, the storage field is required. The available storage environments are the same ones listed in the [Containers](doc:containers) section. This location will also be the destination of that container after runs unless otherwise specified in a protocol. After you've entered your samples, they will be visible in your inventory and useable within protocols, however, runs will notify you that they are "awaiting shipment" and won't be executed until the samples are received. [block:html] { "html": "<div>\n <video style=\"max-width: 100%\" controls>\n \t<source src=\"//static.transcriptic.com/screencasts/populate_inventory.webm\" type=\"video/webm; codecs=vp8\">\n\t <source src=\"//static.transcriptic.com/screencasts/populate_inventory.mp4\" type=\"video/mp4; codecs=avc1.64001f\">\n\t</video>\n</div>" } [/block] ## Step 3: Mail Us Your Samples Each shipment is associated with a four letter intake code, which should be written on the packaging in which you ship us your samples. In addition, each sample (individual tube or plate) has its own 3-letter code which should be written on the container itself. If these codes aren't included, we won't be able to properly insert your samples in inventory and track them. [block:image] { "images": [ { "image": [ "https://files.readme.io/YDFRso9ORiCrNQqo8Vot_Transcriptic_Shipment.png", "Transcriptic_Shipment.png", "860", "977", "#a0145f", "" ] } ] } [/block] [block:image] { "images": [ { "image": [ "https://files.readme.io/fsOXOgjTRy9oyjpeUHFn_Tracking_Number.png", "Tracking_Number.png", "775", "388", "#ca1358", "" ], "caption": "For expedited shipping, a tracking number can be entered on the Intake Kits page of your inventory after your samples have been shipped." } ] } [/block] [block:callout] { "type": "info", "title": "Transcriptic Plates and Tubes", "body": "Only the provided tubes and plates can be used with our platform. Please [contact us](mailto:support@transcriptic.com) if you have samples that cannot conform to the containers currently provided with the intake kit.\n\nPlease do not attach anything to Transcriptic containers. Sticky labels can interfere with the sample in take process. If you need to label your containers please write on the side of them with a permanent marker. \n\nIf you choose to submit your samples in your own containers or send reagents to Transcriptic from a vendor directly, you will be charged an intake fee of $50 per 96 well plate or $50 per 12 tube shipment." } [/block] [block:api-header] { "type": "basic", "title": "Launching a Standard Protocol" } [/block] To launch a standard protocol, navigate to one of your existing projects (or create a new one) and click on "Launch a Run" in the upper right corner. If this is your first run in a project, you can also click the "Browse All Protocols" button. On the dialog that comes up, select the protocol you wish to run. The next screen will present you with parameters you can use to customize your protocol. Any field that requires a Container, Aliquots or Aliquot will bring up the inventory browser, from which you can choose the appropriate object from your inventory. Once you're satisfied with your parameters, click "Next". If the protocol is valid, the next screen will show you an overview of your protocol with the parameters and samples you chose. You can click on each instruction card to see details about what the [Workcell](https://transcriptic.com/workcells) will be doing. If everything looks ok, click "Submit". [block:callout] { "type": "warning", "title": "Protocol Pricing", "body": "Most protocols are priced on a per-reaction basis." } [/block] Congratulations! Your run is now in the queue and will begin execution shortly. You'll get an email when the run begins and when it's completed. If your run generated analytical data, it will be viewable under the Results tab. See the whole process in action below: [block:html] { "html": "<div>\n <video style=\"max-width: 100%\" controls>\n \t<source src=\"//static.transcriptic.com/screencasts/launch_run.webm\" type=\"video/webm; codecs=vp8\">\n\t <source src=\"//static.transcriptic.com/screencasts/launch_run.mp4\" type=\"video/mp4; codecs=avc1.64001f\">\n\t</video>\n</div>" } [/block] [block:api-header] { "type": "basic", "title": "Custom Protocol Implementation" } [/block] If none of the [standard protocols](https://developers.transcriptic.com/v1.0/docs/getting-started#launching-a-standard-protocol) available are sufficient for the experiment you'd like to automate, never fear! We have an experienced team of application scientists that can help you implement a custom protocol. Send us an email at [sales@transcriptic.com](mailto:sales@transcriptic.com) with an outline of the protocol you'd like implemented and we will get back to you with specifics. [block:api-header] { "type": "basic", "title": "Developing Your Own Protocols" } [/block] There are two components to development at Transcriptic. You can develop on the individual protocol level and submit runs [through the command-line](doc:getting-started-with-the-cli). It is suggested that you get your feet wet by first reading up on [Autoprotocol](http://autoprotocol.org), an open-source data standard Transcriptic created to document protocols in a format both humans and our workcells understand. Then, you can browse the [About Autoprotocol](doc:autoprotocol) section to read more about the tools we and others have created to make encoding protocols in Autoprotocol easier. You can also [create a package](doc:what-is-a-package), or a custom user interface for your protocol or group of protocols (like the standard validated protocols shown above). Creating a package is useful for repeatedly launching the same protocol over and over with different samples and/or parameters. Check out the [Package Creation Quickstart](doc:package-creation-quickstart) for more information. There is documentation available [here](http://autoprotocol-python.transcriptic.com/) and [here](http://autoprotocol-utilities.transcriptic.com/) .If you get stuck, a wonderful community of developers is available to help you over in [Our Community](http://forum.transcriptic.com). [block:callout] { "type": "warning", "title": "Developer Disclaimer", "body": "By developing and submitting your own protocols without consulting Transcriptic for code review and protocol validation, you assume responsibility for any troubleshooting required to optimize your protocol for Transcriptic’s automated Workcells. It is highly recommended that you at least read through our [Liquid Handling Design Rules](doc:liquid-handling-guide) and [How to Write a New Protocol](doc:how-to-write-a-new-protocol) sections within this documentation before you begin development." } [/block]