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-<?
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+<?php
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//Include the header
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View::show_header('Uploading Rules', 'rules');
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?>
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@@ -7,12 +7,12 @@ View::show_header('Uploading Rules', 'rules');
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<div class="header">
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<h2>Upload</h2>
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</div>
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-<!-- Uploading Rules Index Links -->
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+ <!-- Uploading Rules Index Links -->
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<br />
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<form class="search_form" name="rules" onsubmit="return false" action="">
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<input type="text" id="search_string" value="Filter (empty to reset)" />
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<span id="Index">Searching for <strong>upload</strong> returns all rules containing that term.
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- Searching for <strong>upload+trump</strong> returns all rules containing both terms</span>
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+ Searching for <strong>upload+trump</strong> returns all rules containing both terms</span>
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</form>
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<br />
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<div class="before_rules">
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</ul>
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</div>
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</div>
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-<!-- Actual Uploading Rules -->
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+ <!-- Actual Uploading Rules -->
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<div id="actual_rules">
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<div class="before_rules">
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<h4 id="Intro"><a href="#Introk"><strong>↑</strong></a> Introduction</h4>
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- <div class="box pad" style="padding: 10px 10px 10px 20px;">
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+ <div class="box pad" style="padding: 10px 10px 10px 20px;">
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<p>
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- <?= SITE_NAME ?> is the global DIYbio community's distributed data repository.
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+ <?= SITE_NAME ?> is the global DIYbio community's
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+ distributed data repository.
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The content includes richly annotated and searchable biological sequence and medical imaging data.
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It follows the example of private BitTorrent sites to
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- <a href="https://www.cambridge.org/core/services/aop-cambridge-core/content/view/2F379FE0CB50DF502F0075119FD3E060/S1744137417000650a.pdf/institutional_solutions_to_freeriding_in_peertopeer_networks_a_case_study_of_online_pirate_communities.pdf" target="_blank">address the free-rider problem</a>
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+ <a href="https://www.cambridge.org/core/services/aop-cambridge-core/content/view/2F379FE0CB50DF502F0075119FD3E060/S1744137417000650a.pdf/institutional_solutions_to_freeriding_in_peertopeer_networks_a_case_study_of_online_pirate_communities.pdf"
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+ target="_blank">address the free-rider problem</a>
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without recourse to institutional funding.
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</p>
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Thanks for taking an interest in this project and contributing to its success.
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Please note that <?= SITE_NAME ?> isn't a pirate website.
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</p>
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- </div>
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+ </div>
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<h4 id="def"><a href="#defk"><strong>↑</strong></a> Definitions</h4>
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<ul>
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- <li><b>Torrent.</b> Broadly used as a noun to describe a <code>.torrent</code> file, the files associated with it, and any associated metadata indexed by the site. Used as a verb to describe the act of downloading or uploading data from or to the swarm.</li>
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+ <li><b>Torrent.</b> Broadly used as a noun to describe a <code>.torrent</code> file, the files associated with
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+ it, and any associated metadata indexed by the site. Used as a verb to describe the act of downloading or
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+ uploading data from or to the swarm.</li>
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<li><b>Swarm.</b> All peers associated with a given torrent.</li>
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<li><b>Peer.</b> A client that has announced to the tracker and is part of the swarm.</b>
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- <li><b>Seed.</b> When used as a verb, describes the act of uploading torrent content to other peers. When used as a noun, describes a peer who has all of content associated with a torrent as is able to upload to peers. Sometimes referred to as a seeder.</li>
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- <li><b>Leech.</b> When used as a verb, describes the act of downloading torrent content from another peer. When used as a noun, describes someone who is downloading or wants to download torrent content from another peer. Sometimes referred to as a leecher.</li>
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- <li><b>Metadata.</b> The information we record here on the site for each torrent, such as title, encoding information, and tags.</li>
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+ <li><b>Seed.</b> When used as a verb, describes the act of uploading torrent content to other peers. When used
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+ as a noun, describes a peer who has all of content associated with a torrent as is able to upload to peers.
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+ Sometimes referred to as a seeder.</li>
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+ <li><b>Leech.</b> When used as a verb, describes the act of downloading torrent content from another peer.
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+ When used as a noun, describes someone who is downloading or wants to download torrent content from another
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+ peer. Sometimes referred to as a leecher.</li>
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+ <li><b>Metadata.</b> The information we record here on the site for each torrent, such as title, encoding
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+ information, and tags.</li>
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<li><b>Hentai.</b> A subgenre of anime, manga, and games characterized by being pornographic.</li>
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</ul>
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<h4 id="hU"><a href="#hUk"><strong>↑</strong></a> <a href="#hU"></a> Upload Rules</h4>
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- <h5 id="h1"><a href="#h1k"><strong>↑</strong></a> <a href="#h1">1</a> General and Formatting</h5>
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- <div class="box pad" style="padding: 10px 10px 10px 20px;">
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+ <h5 id="h1"><a href="#h1k"><strong>↑</strong></a> <a href="#h1">1</a> General and Formatting</h5>
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+ <div class="box pad" style="padding: 10px 10px 10px 20px;">
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+ <ul>
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+ <li id="r1.1"><a href="#h1"><strong>↑</strong></a> <a href="#r1.1">1.1</a>
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+ <strong>Biology Only.</strong>
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+ <?=SITE_NAME?> is an annotated repository of biology data
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+ and a bioinformatics learning community.
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+ Gazelle in its current state requires lots of hardcoded metadata.
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+ I can help you adapt the design, e.g., for physics or astronomy data.
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+ A generalized science tracker is in development.
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+ </li>
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+ <li id="r1.2"><a href="#h1"><strong>↑</strong></a> <a href="#r1.2">1.2</a>
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+ <strong>Seed Forever.</strong>
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+ Private torrent trackers succeed when they offer quality niche content and a comfy interface.
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+ This isn't an NCBI data dump but a library of annotated info hashes that tomorrow's networks can ingest.
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+ Do not upload a torrent unless you intend to seed until there are at least 3 copies.
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+ Three is a good minimum swarm size.
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+ </li>
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+
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+ <li id="r1.3"><a href="#h1"><strong>↑</strong></a> <a href="#r1.3">1.3</a>
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+ <strong>No Advertising.</strong>
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+ Please don't "tag" torrents, include ASCII art, or make your torrents look like they came from the Pirate Bay.
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+ These kinds of additions are allowed if they serve a relevant purpose.
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+ Enclosing a GPG-signed hash of your data isn't a bad idea at all.
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<ul>
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- <li id="r1.1"><a href="#h1"><strong>↑</strong></a> <a href="#r1.1">1.1</a>
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- <strong>Biology Only.</strong>
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- <?=SITE_NAME?> is an annotated repository of biology data and a bioinformatics learning community.
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- Gazelle in its current state requires lots of hardcoded metadata.
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- I can help you adapt the design, e.g., for physics or astronomy data.
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- A generalized science tracker is in development.
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- </li>
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-
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- <li id="r1.2"><a href="#h1"><strong>↑</strong></a> <a href="#r1.2">1.2</a>
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- <strong>Seed Forever.</strong>
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- Private torrent trackers succeed when they offer quality niche content and a comfy interface.
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- This isn't an NCBI data dump but a library of annotated info hashes that tomorrow's networks can ingest.
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- Do not upload a torrent unless you intend to seed until there are at least 3 copies.
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- Three is a good minimum swarm size.
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- </li>
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- <li id="r1.3"><a href="#h1"><strong>↑</strong></a> <a href="#r1.3">1.3</a>
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- <strong>No Advertising.</strong>
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- Please don't "tag" torrents, include ASCII art, or make your torrents look like they came from the Pirate Bay.
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- These kinds of additions are allowed if they serve a relevant purpose.
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- Enclosing a GPG-signed hash of your data isn't a bad idea at all.
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- <ul>
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- </ul>
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- </li>
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- <li id="r1.4"><a href="#h1"><strong>↑</strong></a> <a href="#r1.4">1.4</a>
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- <strong>Speak English.</strong>
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- <?=SITE_NAME?> is an Anglophone site.
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- Everything but private messages, and especially torrents and the forums, should be in English.
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- </li>
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- <li id="r1.5"><a href="#h1"><strong>↑</strong></a> <a href="#r1.5">1.5</a>
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- <strong>Good Data.</strong>
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- Strive to release complete collections of the highest fidelity data in the most sensible format.
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- Sometimes I wonder whether certain kinds of people are drawn to private torrent trackers, or if the site design encourages otherwise disinterested people to do well.
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- </li>
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- <li id="r1.6"><a href="#h1"><strong>↑</strong></a> <a href="#r1.6">1.6</a>
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- <strong>No DRM.</strong>
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- Archived releases must not be password protected.
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- DRM of any kind isn't allowed.
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- </li>
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- <hr style="margin: 2em auto; opacity: 0.3; width: 50%;" />
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- <li id="r1.7"><a href="#h1"><strong>↑</strong></a> <a href="#r1.7">1.7</a>
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- <strong>Folder Structure.</strong>
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- Each torrent should be a single folder so we can manage them easier.
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- Please avoid unnecessary nested folders inside your torrent.
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- Use one of the examples below for your main folder.
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-
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- <ul>
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- <li>One-Shot Project Name</li>
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- <li>Torrent Title - Accession Number</li>
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- <li>Department/Lab - Project Name</li>
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- <li>After the Name - Extra comments as necessary</li>
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- </ul>
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- I also strongly recommend you compress only large files or long image series, and not simply compress the entire dataset.
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- This makes it easier to partially seed large datasets, work with discrete parts of the data, and know what's on disk.
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- </li>
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- <li id="r1.8"><a href="#h1"><strong>↑</strong></a> <a href="#r1.8">1.8</a>
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- <strong>File Organization.</strong>
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- Please either keep the original filenames from the processing service, or consistently use a legible naming scheme.
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- Remove all .DS_Store, Thumbs.db, nfo files, and other junk files before making the torrent.
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- It should be "clean."
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- You're encouraged to keep Git repos, structured data reports, readmes, and other useful annotations.
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- Files should sort appropriately: use leading zeroes.
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- </li>
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- <li id="r1.9"><a href="#h1"><strong>↑</strong></a> <a href="#r1.9">1.9</a>
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- <strong>Compression.</strong>
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- "10 GiB or 10,000 files."
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- Compression is required if your torrent is > 10 GiB or if it contains > 10,000 files.
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- Otherwise, please compress text files if it reduces the torrent size by > 30%.
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- Never compress torrents < 2 GiB or binary files < 10 GiB.
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- Multipart archives are only allowed for torrents > 10 GiB.
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- </li>
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- <li id="r1.10"><a href="#h1"><strong>↑</strong></a> <a href="#r1.10">1.10</a>
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- <strong>Metadata.</strong>
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- Avoid matching folder names to <?=SITE_NAME?> metadata.
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- The site design will change but the torrents are evergreen.
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- When What.cd went down, it was possible to seed most of your old torrents at Redacted.ch because the info hashes matched.
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- The <code>.torrent</code> points to cryptographically verified folders and files that are tracked for convenience.
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- On the flipside, please add enough metadata so that people can pick it out of a list.
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- </li>
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- <li id="r1.11"><a href="#h1"><strong>↑</strong></a> <a href="#r1.11">1.11</a>
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- <strong>Supplemental Packs.</strong>
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- I strongly recommend <a href="https://semver.org/" target="_blank">Semantic Versioning</a> for your original data.
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- Supplemental packs may include a collection of documents, utilities, protocols, metadata, etc., specifically prepared for release.
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- The collection should be a separate torrent if the collection constitutes a project in its own right.
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- But if you have, e.g., 100 MiB of XML and no other metadata for 5 GB of photos, please include it in the main torrent.
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- </li>
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- </div>
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+ </li>
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+ <li id="r1.4"><a href="#h1"><strong>↑</strong></a> <a href="#r1.4">1.4</a>
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+ <strong>Speak English.</strong>
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+ <?=SITE_NAME?> is an Anglophone site.
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+ Everything but private messages, and especially torrents and the forums, should be in English.
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+ </li>
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+
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+ <li id="r1.5"><a href="#h1"><strong>↑</strong></a> <a href="#r1.5">1.5</a>
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+ <strong>Good Data.</strong>
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+ Strive to release complete collections of the highest fidelity data in the most sensible format.
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+ Sometimes I wonder whether certain kinds of people are drawn to private torrent trackers, or if the site
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+ design encourages otherwise disinterested people to do well.
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+ </li>
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+
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+ <li id="r1.6"><a href="#h1"><strong>↑</strong></a> <a href="#r1.6">1.6</a>
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+ <strong>No DRM.</strong>
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+ Archived releases must not be password protected.
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+ DRM of any kind isn't allowed.
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+ </li>
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+
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+ <hr style="margin: 2em auto; opacity: 0.3; width: 50%;" />
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+
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+ <li id="r1.7"><a href="#h1"><strong>↑</strong></a> <a href="#r1.7">1.7</a>
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+ <strong>Folder Structure.</strong>
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+ Each torrent should be a single folder so we can manage them easier.
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+ Please avoid unnecessary nested folders inside your torrent.
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+ Use one of the examples below for your main folder.
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- <h5 id="h2"><a href="#h2k"><strong>↑</strong></a> <a href="#h2">2</a> Duplicates and Trumping</h5>
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- <div class="box pad" style="padding: 10px 10px 10px 20px;">
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<ul>
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- <li id="r2.1"><a href="#h2"><strong>↑</strong></a> <a href="#r2.1">2.1</a>
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- <strong>Multiple Formats Allowed.</strong>
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- It's fine if there's an EMBL and a FASTA of the same data. If you need to convert a dataset for your analysis, please upload a quality conversion with supplemetal info.
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- Remember that small, one-shot metadata are better included with the data, and collections of docs and utils are better separate from it.
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- If only the header is different and it follows the "10 GiB or 10,000 files" rule, uncompressed torrents trump compressed ones.
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- It should be easy for others with the same data to change a line and check out the new torrent.
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- </li>
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- <li id="r2.2"><a href="#h2"><strong>↑</strong></a> <a href="#r2.2">2.2</a>
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- <strong>SemVer Trumps.</strong>
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- Versioned data can be trumped at the patch level.
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- Major and minor releases can coexist.
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191
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- Please add a link in the old data's Torrent Group Description to the new data.
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192
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- Git repos can be trumped at the commit and patch levels.
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- Then normal SemVer rules take effect for properly tagged releases.
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- </li>
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-
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- <li id="r2.3"><a href="#h2"><strong>↑</strong></a> <a href="#r2.3">2.3</a>
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- <strong>Report Trumps and Dupes.</strong>
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198
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- If you trump a torrent or notice a duplicate torrent, please use the report link [RP] to notify staff to remove it.
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- If you are uploading a superior version, e.g., without watermarks, report the older torrent and include a link to your new torrent.
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- Your torrent may be deleted as a dupe if the older torrent is not reported.
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- </li>
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-
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203
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- <li id="r2.4"><a href="#h2"><strong>↑</strong></a> <a href="#r2.4">2.4</a>
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- <strong>Two Weeks Unseeded.</strong>
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- If you have the original torrent files for the inactive torrent, reseed those original files instead of uploading a new torrent.
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- Uploading a replacement torrent should be done only when the original files are unavailable.
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- </li>
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-
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- <li id="r2.5"><a href="#h2"><strong>↑</strong></a> <a href="#r2.5">2.5</a>
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- <strong>Watermarks.</strong>
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- Data without watermarks trumps watermarked data.
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140
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+ <li>One-Shot Project Name</li>
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141
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+ <li>Torrent Title - Accession Number</li>
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142
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+ <li>Department/Lab - Project Name</li>
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+ <li>After the Name - Extra comments as necessary</li>
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144
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</ul>
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- </div>
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145
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- <h5 id="h3"><a href="#h3k"><strong>↑</strong></a> <a href="#h3">3</a> Upload Form Walkthrough</h5>
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216
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- <div class="box pad" style="padding: 10px 10px 10px 20px;">
|
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146
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+ I also strongly recommend you compress only large files or long image series, and not simply compress the
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147
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+ entire dataset.
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148
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+ This makes it easier to partially seed large datasets, work with discrete parts of the data, and know what's
|
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149
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+ on disk.
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150
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+ </li>
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151
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+
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152
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+ <li id="r1.8"><a href="#h1"><strong>↑</strong></a> <a href="#r1.8">1.8</a>
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153
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+ <strong>File Organization.</strong>
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154
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+ Please either keep the original filenames from the processing service, or consistently use a legible naming
|
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155
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+ scheme.
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156
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+ Remove all .DS_Store, Thumbs.db, nfo files, and other junk files before making the torrent.
|
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+ It should be "clean."
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158
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+ You're encouraged to keep Git repos, structured data reports, readmes, and other useful annotations.
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159
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+ Files should sort appropriately: use leading zeroes.
|
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160
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+ </li>
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+
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162
|
+ <li id="r1.9"><a href="#h1"><strong>↑</strong></a> <a href="#r1.9">1.9</a>
|
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163
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+ <strong>Compression.</strong>
|
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164
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+ "10 GiB or 10,000 files."
|
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165
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+ Compression is required if your torrent is > 10 GiB or if it contains > 10,000 files.
|
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166
|
+ Otherwise, please compress text files if it reduces the torrent size by > 30%.
|
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167
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+ Never compress torrents < 2 GiB or binary files < 10 GiB. Multipart archives are only allowed for torrents> 10
|
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168
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+ GiB.
|
|
|
169
|
+ </li>
|
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170
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+
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171
|
+ <li id="r1.10"><a href="#h1"><strong>↑</strong></a> <a href="#r1.10">1.10</a>
|
|
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172
|
+ <strong>Metadata.</strong>
|
|
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173
|
+ Avoid matching folder names to <?=SITE_NAME?> metadata.
|
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174
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+ The site design will change but the torrents are evergreen.
|
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175
|
+ When What.cd went down, it was possible to seed most of your old torrents at Redacted.ch because the info
|
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176
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+ hashes matched.
|
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177
|
+ The <code>.torrent</code> points to cryptographically verified folders and files that are tracked for
|
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178
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+ convenience.
|
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179
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+ On the flipside, please add enough metadata so that people can pick it out of a list.
|
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180
|
+ </li>
|
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181
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+
|
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182
|
+ <li id="r1.11"><a href="#h1"><strong>↑</strong></a> <a href="#r1.11">1.11</a>
|
|
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183
|
+ <strong>Supplemental Packs.</strong>
|
|
|
184
|
+ I strongly recommend <a href="https://semver.org/" target="_blank">Semantic Versioning</a> for your original
|
|
|
185
|
+ data.
|
|
|
186
|
+ Supplemental packs may include a collection of documents, utilities, protocols, metadata, etc., specifically
|
|
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187
|
+ prepared for release.
|
|
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188
|
+ The collection should be a separate torrent if the collection constitutes a project in its own right.
|
|
|
189
|
+ But if you have, e.g., 100 MiB of XML and no other metadata for 5 GB of photos, please include it in the main
|
|
|
190
|
+ torrent.
|
|
|
191
|
+ </li>
|
|
|
192
|
+ </ul>
|
|
|
193
|
+ </div>
|
|
|
194
|
+
|
|
|
195
|
+ <h5 id="h2"><a href="#h2k"><strong>↑</strong></a> <a href="#h2">2</a> Duplicates and Trumping</h5>
|
|
|
196
|
+ <div class="box pad" style="padding: 10px 10px 10px 20px;">
|
|
|
197
|
+ <ul>
|
|
|
198
|
+ <li id="r2.1"><a href="#h2"><strong>↑</strong></a> <a href="#r2.1">2.1</a>
|
|
|
199
|
+ <strong>Multiple Formats Allowed.</strong>
|
|
|
200
|
+ It's fine if there's an EMBL and a FASTA of the same data. If you need to convert a dataset for your analysis,
|
|
|
201
|
+ please upload a quality conversion with supplemetal info.
|
|
|
202
|
+ Remember that small, one-shot metadata are better included with the data, and collections of docs and utils
|
|
|
203
|
+ are better separate from it.
|
|
|
204
|
+ If only the header is different and it follows the "10 GiB or 10,000 files" rule, uncompressed torrents trump
|
|
|
205
|
+ compressed ones.
|
|
|
206
|
+ It should be easy for others with the same data to change a line and check out the new torrent.
|
|
|
207
|
+ </li>
|
|
|
208
|
+
|
|
|
209
|
+ <li id="r2.2"><a href="#h2"><strong>↑</strong></a> <a href="#r2.2">2.2</a>
|
|
|
210
|
+ <strong>SemVer Trumps.</strong>
|
|
|
211
|
+ Versioned data can be trumped at the patch level.
|
|
|
212
|
+ Major and minor releases can coexist.
|
|
|
213
|
+ Please add a link in the old data's Torrent Group Description to the new data.
|
|
|
214
|
+ Git repos can be trumped at the commit and patch levels.
|
|
|
215
|
+ Then normal SemVer rules take effect for properly tagged releases.
|
|
|
216
|
+ </li>
|
|
|
217
|
+
|
|
|
218
|
+ <li id="r2.3"><a href="#h2"><strong>↑</strong></a> <a href="#r2.3">2.3</a>
|
|
|
219
|
+ <strong>Report Trumps and Dupes.</strong>
|
|
|
220
|
+ If you trump a torrent or notice a duplicate torrent, please use the report link [RP] to notify staff to
|
|
|
221
|
+ remove it.
|
|
|
222
|
+ If you are uploading a superior version, e.g., without watermarks, report the older torrent and include a link
|
|
|
223
|
+ to your new torrent.
|
|
|
224
|
+ Your torrent may be deleted as a dupe if the older torrent is not reported.
|
|
|
225
|
+ </li>
|
|
|
226
|
+
|
|
|
227
|
+ <li id="r2.4"><a href="#h2"><strong>↑</strong></a> <a href="#r2.4">2.4</a>
|
|
|
228
|
+ <strong>Two Weeks Unseeded.</strong>
|
|
|
229
|
+ If you have the original torrent files for the inactive torrent, reseed those original files instead of
|
|
|
230
|
+ uploading a new torrent.
|
|
|
231
|
+ Uploading a replacement torrent should be done only when the original files are unavailable.
|
|
|
232
|
+ </li>
|
|
|
233
|
+
|
|
|
234
|
+ <li id="r2.5"><a href="#h2"><strong>↑</strong></a> <a href="#r2.5">2.5</a>
|
|
|
235
|
+ <strong>Watermarks.</strong>
|
|
|
236
|
+ Data without watermarks trumps watermarked data.
|
|
|
237
|
+ </ul>
|
|
|
238
|
+ </div>
|
|
|
239
|
+
|
|
|
240
|
+ <h5 id="h3"><a href="#h3k"><strong>↑</strong></a> <a href="#h3">3</a> Upload Form Walkthrough</h5>
|
|
|
241
|
+ <div class="box pad" style="padding: 10px 10px 10px 20px;">
|
|
|
242
|
+ <ul>
|
|
|
243
|
+ <li id="r3.1"><a href="#h3"><strong>↑</strong></a> <a href="#r3.1">3.1</a>
|
|
|
244
|
+ <strong>Torrent File.</strong>
|
|
|
245
|
+ Add the announce URL as the only item on the tracker list and click the checkbox marked private.
|
|
|
246
|
+ Please don't share <code>.torrent</code> files because they have your passkey embedded in them.
|
|
|
247
|
+ This passkey lets the tracker know who's uploading and downloading, and leaking it will nuke your ratio.
|
|
|
248
|
+ <br /><br />
|
|
|
249
|
+ </li>
|
|
|
250
|
+
|
|
|
251
|
+ <li id="r3.2"><a href="#h3"><strong>↑</strong></a> <a href="#r3.2">3.2</a>
|
|
|
252
|
+ <strong>Type.</strong>
|
|
|
253
|
+ The categories loosely follow the central dogma.
|
|
|
254
|
+ It depends on what alphabet the sequence uses, e.g., ACGT vs. ACGU.
|
|
|
255
|
+ All medical imaging data goes in the Imaging category.
|
|
|
256
|
+ All extra documentation, custom scripts, etc., goes in Documents.
|
|
|
257
|
+ Plasmids and things that don't quite fit go in Other.
|
|
|
258
|
+ <br /><br />
|
|
|
259
|
+ </li>
|
|
|
260
|
+
|
|
|
261
|
+ <li id="r3.3"><a href="#h3"><strong>↑</strong></a> <a href="#r3.3">3.3</a>
|
|
|
262
|
+ <strong>Accession Number.</strong>
|
|
|
263
|
+ Please add accession numbers when the data source issued them.
|
|
|
264
|
+ The number can be any format but it must correspond to the actual torrent data.
|
|
|
265
|
+ Don't add accession numbers just because the metadata matches.
|
|
|
266
|
+ RefSeq and UniProt integration is in development.
|
|
|
267
|
+ <br /><br />
|
|
|
268
|
+ </li>
|
|
|
269
|
+
|
|
|
270
|
+ <li id="r3.4"><a href="#h3"><strong>↑</strong></a> <a href="#r3.4">3.4</a>
|
|
|
271
|
+ <strong>Torrent Title.</strong>
|
|
|
272
|
+ A short description of the torrent contents.
|
|
|
273
|
+ It doesn't need to match the folders but it should tell you what the data is at a glance.
|
|
|
274
|
+ Please avoid adding other metadata such as Strain, Platform, etc., with a dedicated field.
|
|
|
275
|
+ <br /><br />
|
|
|
276
|
+ </li>
|
|
|
277
|
+
|
|
|
278
|
+ <li id="r3.5"><a href="#h3"><strong>↑</strong></a> <a href="#r3.5">3.5</a>
|
|
|
279
|
+ <strong>Organism.</strong>
|
|
|
280
|
+ The relevant organism's binomial name and optional subspecies.
|
|
|
281
|
+ Please use <em>Genus species subspecies</em> and no terms such as var. and subsp.
|
|
|
282
|
+ Multiple organisms and a FASTA/GenBank parser are both in development.
|
|
|
283
|
+ <br /><br />
|
|
|
284
|
+ </li>
|
|
|
285
|
+
|
|
|
286
|
+ <li id="r3.6"><a href="#h3"><strong>↑</strong></a> <a href="#r3.6">3.6</a>
|
|
|
287
|
+ <strong>Strain/Variety.</strong>
|
|
|
288
|
+ The strain's name if known.
|
|
|
289
|
+ This should correspond to a specific cell line or breed.
|
|
|
290
|
+ Otherwise, please omit it.
|
|
|
291
|
+ <br /><br />
|
|
|
292
|
+ </li>
|
|
|
293
|
+
|
|
|
294
|
+ <li id="r3.7"><a href="#h3"><strong>↑</strong></a> <a href="#r3.7">3.7</a>
|
|
|
295
|
+ <strong>Authors(s).</strong>
|
|
|
296
|
+ The Author field should contain only the author name.
|
|
|
297
|
+ The upload form supports multiple authors.
|
|
|
298
|
+ Do a search before uploading to get their names right.
|
|
|
299
|
+ Consistent author naming makes browsing easier because it groups torrents on a common page.
|
|
|
300
|
+ ORCiD integration is in development.
|
|
|
301
|
+ <br /><br />
|
|
|
302
|
+ </li>
|
|
|
303
|
+
|
|
|
304
|
+ <li id="r3.8"><a href="#h3"><strong>↑</strong></a> <a href="#r3.8">3.8</a>
|
|
|
305
|
+ <strong>Department/Lab.</strong>
|
|
|
306
|
+ The lab that did the experiments or the last author's home lab.
|
|
|
307
|
+ Please use "Unaffiliated" for anonymous or unknown labs.
|
|
|
308
|
+ <br /><br />
|
|
|
309
|
+ </li>
|
|
|
310
|
+
|
|
|
311
|
+ <li id="r3.9"><a href="#h3"><strong>↑</strong></a> <a href="#r3.9">3.9</a>
|
|
|
312
|
+ <strong>Location.</strong>
|
|
|
313
|
+ The lab's physical location in one of the below formats.
|
|
217
|
314
|
<ul>
|
|
218
|
|
- <li id="r3.1"><a href="#h3"><strong>↑</strong></a> <a href="#r3.1">3.1</a>
|
|
219
|
|
- <strong>Torrent File.</strong>
|
|
220
|
|
- Add the announce URL as the only item on the tracker list and click the checkbox marked private.
|
|
221
|
|
- Please don't share <code>.torrent</code> files because they have your passkey embedded in them.
|
|
222
|
|
- This passkey lets the tracker know who's uploading and downloading, and leaking it will nuke your ratio.
|
|
223
|
|
- <br /><br />
|
|
224
|
|
-</li>
|
|
225
|
|
-
|
|
226
|
|
-<li id="r3.2"><a href="#h3"><strong>↑</strong></a> <a href="#r3.2">3.2</a>
|
|
227
|
|
- <strong>Type.</strong>
|
|
228
|
|
- The categories loosely follow the central dogma.
|
|
229
|
|
- It depends on what alphabet the sequence uses, e.g., ACGT vs. ACGU.
|
|
230
|
|
- All medical imaging data goes in the Imaging category.
|
|
231
|
|
- All extra documentation, custom scripts, etc., goes in Documents.
|
|
232
|
|
- Plasmids and things that don't quite fit go in Other.
|
|
233
|
|
- <br /><br />
|
|
234
|
|
-</li>
|
|
235
|
|
-
|
|
236
|
|
-<li id="r3.3"><a href="#h3"><strong>↑</strong></a> <a href="#r3.3">3.3</a>
|
|
237
|
|
- <strong>Accession Number.</strong>
|
|
238
|
|
- Please add accession numbers when the data source issued them.
|
|
239
|
|
- The number can be any format but it must correspond to the actual torrent data.
|
|
240
|
|
- Don't add accession numbers just because the metadata matches.
|
|
241
|
|
- RefSeq and UniProt integration is in development.
|
|
242
|
|
- <br /><br />
|
|
243
|
|
-</li>
|
|
244
|
|
-
|
|
245
|
|
-<li id="r3.4"><a href="#h3"><strong>↑</strong></a> <a href="#r3.4">3.4</a>
|
|
246
|
|
- <strong>Torrent Title.</strong>
|
|
247
|
|
- A short description of the torrent contents.
|
|
248
|
|
- It doesn't need to match the folders but it should tell you what the data is at a glance.
|
|
249
|
|
- Please avoid adding other metadata such as Strain, Platform, etc., with a dedicated field.
|
|
250
|
|
- <br /><br />
|
|
251
|
|
-</li>
|
|
252
|
|
-
|
|
253
|
|
-<li id="r3.5"><a href="#h3"><strong>↑</strong></a> <a href="#r3.5">3.5</a>
|
|
254
|
|
- <strong>Organism.</strong>
|
|
255
|
|
- The relevant organism's binomial name and optional subspecies.
|
|
256
|
|
- Please use <em>Genus species subspecies</em> and no terms such as var. and subsp.
|
|
257
|
|
- Multiple organisms and a FASTA/GenBank parser are both in development.
|
|
258
|
|
- <br /><br />
|
|
259
|
|
-</li>
|
|
260
|
|
-
|
|
261
|
|
-<li id="r3.6"><a href="#h3"><strong>↑</strong></a> <a href="#r3.6">3.6</a>
|
|
262
|
|
- <strong>Strain/Variety.</strong>
|
|
263
|
|
- The strain's name if known.
|
|
264
|
|
- This should correspond to a specific cell line or breed.
|
|
265
|
|
- Otherwise, please omit it.
|
|
266
|
|
- <br /><br />
|
|
267
|
|
-</li>
|
|
268
|
|
-
|
|
269
|
|
-<li id="r3.7"><a href="#h3"><strong>↑</strong></a> <a href="#r3.7">3.7</a>
|
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270
|
|
- <strong>Authors(s).</strong>
|
|
271
|
|
- The Author field should contain only the author name.
|
|
272
|
|
- The upload form supports multiple authors.
|
|
273
|
|
- Do a search before uploading to get their names right.
|
|
274
|
|
- Consistent author naming makes browsing easier because it groups torrents on a common page.
|
|
275
|
|
- ORCiD integration is in development.
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- <a href="forums.php?action=viewforum&forumid=<?= SUGGESTIONS_FORUM_ID ?>">Please post in the suggestions forum</a>
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- What programs do you need to work with the data?
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- <a href="forums.php?action=viewforum&forumid=<?= SUGGESTIONS_FORUM_ID ?>">Please post in the suggestions forum</a>
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321
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- Please use the Other option if you'd like to enter a resolution such as "420 subjects."
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- <br /><br />
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-<li id="r3.14"><a href="#h3"><strong>↑</strong></a> <a href="#r3.14">3.14</a>
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338
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- <strong>License.</strong>
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339
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- <?= SITE_NAME ?> only allows permissive licenses.
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- If your data is original, please consider licensing it under one of the available options.
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341
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- The "Unknown" option is for compatibility with existing releases.
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342
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- <br /><br />
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343
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-</li>
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344
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-
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345
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-<li id="r3.15"><a href="#h3"><strong>↑</strong></a> <a href="#r3.15">3.15</a>
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346
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- <strong>Tags.</strong>
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347
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348
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- Don't use irrelevant tags, and consider making new tags as a last resort.
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349
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- <a href="forums.php?action=viewforum&forumid=<?= SUGGESTIONS_FORUM_ID ?>">Please post in the suggestions forum</a>
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350
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- if you'd like to request a new official tag.
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351
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- <br /><br />
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352
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-</li>
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353
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-
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354
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-<li id="r3.16"><a href="#h3"><strong>↑</strong></a> <a href="#r3.16">3.16</a>
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355
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- <strong>Picture.</strong>
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356
|
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- Please upload a meaningful picture, especially if you plan to add the torrent to a collection.
|
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357
|
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- A photo of the sequence sample or a representative photo of the organism; an example (preferably not a thumbnail collection) from an imaging dataset;
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358
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- a screenshot of a useful table from the publication; or another similarly informative picture.
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359
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- <br /><br />
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360
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-</li>
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361
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-
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362
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-<li id="r3.17"><a href="#h3"><strong>↑</strong></a> <a href="#r3.17">3.17</a>
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363
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- <strong>Publications.</strong>
|
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364
|
|
- DOI numbers should be well-formed, one per line.
|
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365
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- The system currently discards malformed DOI numbers instead of extracting them from arbitrary strings.
|
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366
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- An auto-extract feature is in development.
|
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367
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- If your research is a URI, please use the Torrent Group Description field.
|
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368
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- <br /><br />
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369
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-</li>
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370
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-
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371
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-<li id="r3.18"><a href="#h3"><strong>↑</strong></a> <a href="#r3.18">3.18</a>
|
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372
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- <strong>Torrent Group Description.</strong>
|
|
373
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- General info about the object of study's function or significance.
|
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374
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- This is the main body text on a torrent's page.
|
|
375
|
|
- Please limit the contents of this field to concise and interesting knowledge.
|
|
376
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- <br /><br />
|
|
377
|
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-</li>
|
|
378
|
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-
|
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379
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|
-<li id="r3.19"><a href="#h3"><strong>↑</strong></a> <a href="#r3.19">3.19</a>
|
|
380
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- <strong>Torrent Description.</strong>
|
|
381
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- Specific info about the protocols and equipment relevant to <em>this</em> data.
|
|
382
|
|
- This text is hidden by default.
|
|
383
|
|
- It displays when you click the Torrent Title next to [ DL | ... | PL ].
|
|
384
|
|
- Please discuss materials and methods here.
|
|
385
|
|
- <br /><br />
|
|
386
|
|
-</li>
|
|
387
|
|
-
|
|
388
|
|
-<li id="r3.20"><a href="#h3"><strong>↑</strong></a> <a href="#r3.20">3.20</a>
|
|
389
|
|
- <strong>Aligned Sequence.</strong>
|
|
390
|
|
- Does the data come with any metadata of an analytical nature, such as alignment data (mandatory)?
|
|
391
|
|
- If so, does the torrent folder contain the scripts used to generate the metadata (optional)?
|
|
392
|
|
- <br /><br />
|
|
393
|
|
-</li>
|
|
394
|
|
-
|
|
395
|
|
-<li id="r3.21"><a href="#h3"><strong>↑</strong></a> <a href="#r3.21">3.21</a>
|
|
396
|
|
- <strong>Upload Anonymously.</strong>
|
|
397
|
|
- You'll still get upload credit even if you hide your username from the torrent details.
|
|
398
|
|
- I believe it's still visible to sysops.
|
|
399
|
|
- </li>
|
|
|
315
|
+ <li>{City}, {State} {Postal Code}</li>
|
|
|
316
|
+ <li>{Postal Code} {City}, {Country}</li>
|
|
400
|
317
|
</ul>
|
|
|
318
|
+ For example, Berkeley, CA 94720 or 10117 Berlin, Germany.
|
|
|
319
|
+ It's okay to use the American style if the foreign address uses the same format.
|
|
|
320
|
+ Please use "Unknown" for anonymous or unknown labs.
|
|
|
321
|
+ <br /><br />
|
|
|
322
|
+ </li>
|
|
|
323
|
+
|
|
|
324
|
+ <li id="r3.10"><a href="#h3"><strong>↑</strong></a> <a href="#r3.10">3.10</a>
|
|
|
325
|
+ <strong>Year.</strong>
|
|
|
326
|
+ The year the data was first published.
|
|
|
327
|
+ The publication that announced the data.
|
|
|
328
|
+ <br /><br />
|
|
|
329
|
+ </li>
|
|
|
330
|
+
|
|
|
331
|
+ <li id="r3.11"><a href="#h3"><strong>↑</strong></a> <a href="#r3.11">3.11</a>
|
|
|
332
|
+ <strong>Platform.</strong>
|
|
|
333
|
+ The class of technology the data comes from.
|
|
|
334
|
+ What sequencing or imaging technique is it the output of?
|
|
|
335
|
+ <a
|
|
|
336
|
+ href="forums.php?action=viewforum&forumid=<?= SUGGESTIONS_FORUM_ID ?>">Please
|
|
|
337
|
+ post in the suggestions forum</a>
|
|
|
338
|
+ if you'd like to request a new platform.
|
|
|
339
|
+ Note that the platforms change for the Imaging category.
|
|
|
340
|
+ <br /><br />
|
|
|
341
|
+ </li>
|
|
|
342
|
+
|
|
|
343
|
+ <li id="r3.12"><a href="#h3"><strong>↑</strong></a> <a href="#r3.12">3.12</a>
|
|
|
344
|
+ <strong>Format.</strong>
|
|
|
345
|
+ The file format of the data.
|
|
|
346
|
+ What programs do you need to work with the data?
|
|
|
347
|
+ <a
|
|
|
348
|
+ href="forums.php?action=viewforum&forumid=<?= SUGGESTIONS_FORUM_ID ?>">Please
|
|
|
349
|
+ post in the suggestions forum</a>
|
|
|
350
|
+ if you'd like to request a new format.
|
|
|
351
|
+ Note that the formats change for the Imaging category.
|
|
|
352
|
+ A file extension parser is in development.
|
|
|
353
|
+ <br /><br />
|
|
|
354
|
+ </li>
|
|
|
355
|
+
|
|
|
356
|
+ <li id="r3.13"><a href="#h3"><strong>↑</strong></a> <a href="#r3.13">3.13</a>
|
|
|
357
|
+ <strong>Assembly Level.</strong>
|
|
|
358
|
+ The resolution of the data.
|
|
|
359
|
+ How much information about the organism does it represent?
|
|
|
360
|
+ The options correspond in higher conceptual language to:
|
|
|
361
|
+ a single piece of information, structural information, especially deep or broad information, and an exhaustive
|
|
|
362
|
+ source.
|
|
|
363
|
+ Please use the Other option if you'd like to enter a resolution such as "420 subjects."
|
|
|
364
|
+ <br /><br />
|
|
|
365
|
+ </li>
|
|
|
366
|
+
|
|
|
367
|
+ <li id="r3.14"><a href="#h3"><strong>↑</strong></a> <a href="#r3.14">3.14</a>
|
|
|
368
|
+ <strong>License.</strong>
|
|
|
369
|
+ <?= SITE_NAME ?> only allows permissive licenses.
|
|
|
370
|
+ If your data is original, please consider licensing it under one of the available options.
|
|
|
371
|
+ The "Unspecified" option is for compatibility with existing releases.
|
|
|
372
|
+ <br /><br />
|
|
|
373
|
+ </li>
|
|
|
374
|
+
|
|
|
375
|
+ <li id="r3.15"><a href="#h3"><strong>↑</strong></a> <a href="#r3.15">3.15</a>
|
|
|
376
|
+ <strong>Tags.</strong>
|
|
|
377
|
+ Please select at least five appropriate tags.
|
|
|
378
|
+ Don't use irrelevant tags, and consider making new tags as a last resort.
|
|
|
379
|
+ <a
|
|
|
380
|
+ href="forums.php?action=viewforum&forumid=<?= SUGGESTIONS_FORUM_ID ?>">Please
|
|
|
381
|
+ post in the suggestions forum</a>
|
|
|
382
|
+ if you'd like to request a new official tag.
|
|
|
383
|
+ <br /><br />
|
|
|
384
|
+ </li>
|
|
|
385
|
+
|
|
|
386
|
+ <li id="r3.16"><a href="#h3"><strong>↑</strong></a> <a href="#r3.16">3.16</a>
|
|
|
387
|
+ <strong>Picture.</strong>
|
|
|
388
|
+ Please upload a meaningful picture, especially if you plan to add the torrent to a collection.
|
|
|
389
|
+ A photo of the sequence sample or a representative photo of the organism; an example (preferably not a
|
|
|
390
|
+ thumbnail collection) from an imaging dataset;
|
|
|
391
|
+ a screenshot of a useful table from the publication; or another similarly informative picture.
|
|
|
392
|
+ <br /><br />
|
|
|
393
|
+ </li>
|
|
|
394
|
+
|
|
|
395
|
+ <li id="r3.17"><a href="#h3"><strong>↑</strong></a> <a href="#r3.17">3.17</a>
|
|
|
396
|
+ <strong>Publications.</strong>
|
|
|
397
|
+ DOI numbers should be well-formed, one per line.
|
|
|
398
|
+ The system currently discards malformed DOI numbers instead of extracting them from arbitrary strings.
|
|
|
399
|
+ An auto-extract feature is in development.
|
|
|
400
|
+ If your research is a URI, please use the Torrent Group Description field.
|
|
|
401
|
+ <br /><br />
|
|
|
402
|
+ </li>
|
|
401
|
403
|
|
|
|
404
|
+ <li id="r3.18"><a href="#h3"><strong>↑</strong></a> <a href="#r3.18">3.18</a>
|
|
|
405
|
+ <strong>Torrent Group Description.</strong>
|
|
|
406
|
+ General info about the object of study's function or significance.
|
|
|
407
|
+ This is the main body text on a torrent's page.
|
|
|
408
|
+ Please limit the contents of this field to concise and interesting knowledge.
|
|
|
409
|
+ <br /><br />
|
|
|
410
|
+ </li>
|
|
|
411
|
+
|
|
|
412
|
+ <li id="r3.19"><a href="#h3"><strong>↑</strong></a> <a href="#r3.19">3.19</a>
|
|
|
413
|
+ <strong>Torrent Description.</strong>
|
|
|
414
|
+ Specific info about the protocols and equipment relevant to <em>this</em> data.
|
|
|
415
|
+ This text is hidden by default.
|
|
|
416
|
+ It displays when you click the Torrent Title next to [ DL | ... | PL ].
|
|
|
417
|
+ Please discuss materials and methods here.
|
|
|
418
|
+ <br /><br />
|
|
|
419
|
+ </li>
|
|
|
420
|
+
|
|
|
421
|
+ <li id="r3.20"><a href="#h3"><strong>↑</strong></a> <a href="#r3.20">3.20</a>
|
|
|
422
|
+ <strong>Aligned Sequence.</strong>
|
|
|
423
|
+ Does the data come with any metadata of an analytical nature, such as alignment data (mandatory)?
|
|
|
424
|
+ If so, does the torrent folder contain the scripts used to generate the metadata (optional)?
|
|
|
425
|
+ <br /><br />
|
|
|
426
|
+ </li>
|
|
|
427
|
+
|
|
|
428
|
+ <li id="r3.21"><a href="#h3"><strong>↑</strong></a> <a href="#r3.21">3.21</a>
|
|
|
429
|
+ <strong>Upload Anonymously.</strong>
|
|
|
430
|
+ You'll still get upload credit even if you hide your username from the torrent details.
|
|
|
431
|
+ I believe it's still visible to sysops.
|
|
|
432
|
+ </li>
|
|
|
433
|
+ </ul>
|
|
|
434
|
+
|
|
|
435
|
+ </div>
|
|
|
436
|
+ <!-- END Other Sections -->
|
|
|
437
|
+ <?php include('jump.php'); ?>
|
|
402
|
438
|
</div>
|
|
403
|
|
-<!-- END Other Sections -->
|
|
404
|
|
-<? include('jump.php'); ?>
|
|
405
|
|
-</div>
|
|
406
|
|
-<?
|
|
|
439
|
+ <?php
|
|
407
|
440
|
View::show_footer();
|
|
408
|
|
-?>
|
pjc
5 years ago