├── .gitignore ├── LICENSE ├── README.md └── preprint ├── .gitignore ├── preprint.bib ├── preprint.tex └── wlpeerj.cls /.gitignore: -------------------------------------------------------------------------------- 1 | *~ 2 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | Attribution 4.0 International 2 | 3 | ======================================================================= 4 | 5 | Creative Commons Corporation ("Creative Commons") is not a law firm and 6 | does not provide legal services or legal advice. Distribution of 7 | Creative Commons public licenses does not create a lawyer-client or 8 | other relationship. Creative Commons makes its licenses and related 9 | information available on an "as-is" basis. Creative Commons gives no 10 | warranties regarding its licenses, any material licensed under their 11 | terms and conditions, or any related information. Creative Commons 12 | disclaims all liability for damages resulting from their use to the 13 | fullest extent possible. 14 | 15 | Using Creative Commons Public Licenses 16 | 17 | Creative Commons public licenses provide a standard set of terms and 18 | conditions that creators and other rights holders may use to share 19 | original works of authorship and other material subject to copyright 20 | and certain other rights specified in the public license below. The 21 | following considerations are for informational purposes only, are not 22 | exhaustive, and do not form part of our licenses. 23 | 24 | Considerations for licensors: Our public licenses are 25 | intended for use by those authorized to give the public 26 | permission to use material in ways otherwise restricted by 27 | copyright and certain other rights. Our licenses are 28 | irrevocable. Licensors should read and understand the terms 29 | and conditions of the license they choose before applying it. 30 | Licensors should also secure all rights necessary before 31 | applying our licenses so that the public can reuse the 32 | material as expected. Licensors should clearly mark any 33 | material not subject to the license. This includes other CC- 34 | licensed material, or material used under an exception or 35 | limitation to copyright. More considerations for licensors: 36 | wiki.creativecommons.org/Considerations_for_licensors 37 | 38 | Considerations for the public: By using one of our public 39 | licenses, a licensor grants the public permission to use the 40 | licensed material under specified terms and conditions. If 41 | the licensor's permission is not necessary for any reason--for 42 | example, because of any applicable exception or limitation to 43 | copyright--then that use is not regulated by the license. Our 44 | licenses grant only permissions under copyright and certain 45 | other rights that a licensor has authority to grant. Use of 46 | the licensed material may still be restricted for other 47 | reasons, including because others have copyright or other 48 | rights in the material. A licensor may make special requests, 49 | such as asking that all changes be marked or described. 50 | Although not required by our licenses, you are encouraged to 51 | respect those requests where reasonable. More_considerations 52 | for the public: 53 | wiki.creativecommons.org/Considerations_for_licensees 54 | 55 | ======================================================================= 56 | 57 | Creative Commons Attribution 4.0 International Public License 58 | 59 | By exercising the Licensed Rights (defined below), You accept and agree 60 | to be bound by the terms and conditions of this Creative Commons 61 | Attribution 4.0 International Public License ("Public License"). To the 62 | extent this Public License may be interpreted as a contract, You are 63 | granted the Licensed Rights in consideration of Your acceptance of 64 | these terms and conditions, and the Licensor grants You such rights in 65 | consideration of benefits the Licensor receives from making the 66 | Licensed Material available under these terms and conditions. 67 | 68 | 69 | Section 1 -- Definitions. 70 | 71 | a. Adapted Material means material subject to Copyright and Similar 72 | Rights that is derived from or based upon the Licensed Material 73 | and in which the Licensed Material is translated, altered, 74 | arranged, transformed, or otherwise modified in a manner requiring 75 | permission under the Copyright and Similar Rights held by the 76 | Licensor. For purposes of this Public License, where the Licensed 77 | Material is a musical work, performance, or sound recording, 78 | Adapted Material is always produced where the Licensed Material is 79 | synched in timed relation with a moving image. 80 | 81 | b. Adapter's License means the license You apply to Your Copyright 82 | and Similar Rights in Your contributions to Adapted Material in 83 | accordance with the terms and conditions of this Public License. 84 | 85 | c. Copyright and Similar Rights means copyright and/or similar rights 86 | closely related to copyright including, without limitation, 87 | performance, broadcast, sound recording, and Sui Generis Database 88 | Rights, without regard to how the rights are labeled or 89 | categorized. For purposes of this Public License, the rights 90 | specified in Section 2(b)(1)-(2) are not Copyright and Similar 91 | Rights. 92 | 93 | d. Effective Technological Measures means those measures that, in the 94 | absence of proper authority, may not be circumvented under laws 95 | fulfilling obligations under Article 11 of the WIPO Copyright 96 | Treaty adopted on December 20, 1996, and/or similar international 97 | agreements. 98 | 99 | e. Exceptions and Limitations means fair use, fair dealing, and/or 100 | any other exception or limitation to Copyright and Similar Rights 101 | that applies to Your use of the Licensed Material. 102 | 103 | f. Licensed Material means the artistic or literary work, database, 104 | or other material to which the Licensor applied this Public 105 | License. 106 | 107 | g. Licensed Rights means the rights granted to You subject to the 108 | terms and conditions of this Public License, which are limited to 109 | all Copyright and Similar Rights that apply to Your use of the 110 | Licensed Material and that the Licensor has authority to license. 111 | 112 | h. Licensor means the individual(s) or entity(ies) granting rights 113 | under this Public License. 114 | 115 | i. Share means to provide material to the public by any means or 116 | process that requires permission under the Licensed Rights, such 117 | as reproduction, public display, public performance, distribution, 118 | dissemination, communication, or importation, and to make material 119 | available to the public including in ways that members of the 120 | public may access the material from a place and at a time 121 | individually chosen by them. 122 | 123 | j. Sui Generis Database Rights means rights other than copyright 124 | resulting from Directive 96/9/EC of the European Parliament and of 125 | the Council of 11 March 1996 on the legal protection of databases, 126 | as amended and/or succeeded, as well as other essentially 127 | equivalent rights anywhere in the world. 128 | 129 | k. You means the individual or entity exercising the Licensed Rights 130 | under this Public License. Your has a corresponding meaning. 131 | 132 | 133 | Section 2 -- Scope. 134 | 135 | a. License grant. 136 | 137 | 1. Subject to the terms and conditions of this Public License, 138 | the Licensor hereby grants You a worldwide, royalty-free, 139 | non-sublicensable, non-exclusive, irrevocable license to 140 | exercise the Licensed Rights in the Licensed Material to: 141 | 142 | a. reproduce and Share the Licensed Material, in whole or 143 | in part; and 144 | 145 | b. produce, reproduce, and Share Adapted Material. 146 | 147 | 2. Exceptions and Limitations. For the avoidance of doubt, where 148 | Exceptions and Limitations apply to Your use, this Public 149 | License does not apply, and You do not need to comply with 150 | its terms and conditions. 151 | 152 | 3. Term. The term of this Public License is specified in Section 153 | 6(a). 154 | 155 | 4. Media and formats; technical modifications allowed. The 156 | Licensor authorizes You to exercise the Licensed Rights in 157 | all media and formats whether now known or hereafter created, 158 | and to make technical modifications necessary to do so. The 159 | Licensor waives and/or agrees not to assert any right or 160 | authority to forbid You from making technical modifications 161 | necessary to exercise the Licensed Rights, including 162 | technical modifications necessary to circumvent Effective 163 | Technological Measures. For purposes of this Public License, 164 | simply making modifications authorized by this Section 2(a) 165 | (4) never produces Adapted Material. 166 | 167 | 5. Downstream recipients. 168 | 169 | a. Offer from the Licensor -- Licensed Material. Every 170 | recipient of the Licensed Material automatically 171 | receives an offer from the Licensor to exercise the 172 | Licensed Rights under the terms and conditions of this 173 | Public License. 174 | 175 | b. No downstream restrictions. You may not offer or impose 176 | any additional or different terms or conditions on, or 177 | apply any Effective Technological Measures to, the 178 | Licensed Material if doing so restricts exercise of the 179 | Licensed Rights by any recipient of the Licensed 180 | Material. 181 | 182 | 6. No endorsement. Nothing in this Public License constitutes or 183 | may be construed as permission to assert or imply that You 184 | are, or that Your use of the Licensed Material is, connected 185 | with, or sponsored, endorsed, or granted official status by, 186 | the Licensor or others designated to receive attribution as 187 | provided in Section 3(a)(1)(A)(i). 188 | 189 | b. Other rights. 190 | 191 | 1. Moral rights, such as the right of integrity, are not 192 | licensed under this Public License, nor are publicity, 193 | privacy, and/or other similar personality rights; however, to 194 | the extent possible, the Licensor waives and/or agrees not to 195 | assert any such rights held by the Licensor to the limited 196 | extent necessary to allow You to exercise the Licensed 197 | Rights, but not otherwise. 198 | 199 | 2. Patent and trademark rights are not licensed under this 200 | Public License. 201 | 202 | 3. To the extent possible, the Licensor waives any right to 203 | collect royalties from You for the exercise of the Licensed 204 | Rights, whether directly or through a collecting society 205 | under any voluntary or waivable statutory or compulsory 206 | licensing scheme. In all other cases the Licensor expressly 207 | reserves any right to collect such royalties. 208 | 209 | 210 | Section 3 -- License Conditions. 211 | 212 | Your exercise of the Licensed Rights is expressly made subject to the 213 | following conditions. 214 | 215 | a. Attribution. 216 | 217 | 1. If You Share the Licensed Material (including in modified 218 | form), You must: 219 | 220 | a. retain the following if it is supplied by the Licensor 221 | with the Licensed Material: 222 | 223 | i. identification of the creator(s) of the Licensed 224 | Material and any others designated to receive 225 | attribution, in any reasonable manner requested by 226 | the Licensor (including by pseudonym if 227 | designated); 228 | 229 | ii. a copyright notice; 230 | 231 | iii. a notice that refers to this Public License; 232 | 233 | iv. a notice that refers to the disclaimer of 234 | warranties; 235 | 236 | v. a URI or hyperlink to the Licensed Material to the 237 | extent reasonably practicable; 238 | 239 | b. indicate if You modified the Licensed Material and 240 | retain an indication of any previous modifications; and 241 | 242 | c. indicate the Licensed Material is licensed under this 243 | Public License, and include the text of, or the URI or 244 | hyperlink to, this Public License. 245 | 246 | 2. You may satisfy the conditions in Section 3(a)(1) in any 247 | reasonable manner based on the medium, means, and context in 248 | which You Share the Licensed Material. For example, it may be 249 | reasonable to satisfy the conditions by providing a URI or 250 | hyperlink to a resource that includes the required 251 | information. 252 | 253 | 3. If requested by the Licensor, You must remove any of the 254 | information required by Section 3(a)(1)(A) to the extent 255 | reasonably practicable. 256 | 257 | 4. If You Share Adapted Material You produce, the Adapter's 258 | License You apply must not prevent recipients of the Adapted 259 | Material from complying with this Public License. 260 | 261 | 262 | Section 4 -- Sui Generis Database Rights. 263 | 264 | Where the Licensed Rights include Sui Generis Database Rights that 265 | apply to Your use of the Licensed Material: 266 | 267 | a. for the avoidance of doubt, Section 2(a)(1) grants You the right 268 | to extract, reuse, reproduce, and Share all or a substantial 269 | portion of the contents of the database; 270 | 271 | b. if You include all or a substantial portion of the database 272 | contents in a database in which You have Sui Generis Database 273 | Rights, then the database in which You have Sui Generis Database 274 | Rights (but not its individual contents) is Adapted Material; and 275 | 276 | c. You must comply with the conditions in Section 3(a) if You Share 277 | all or a substantial portion of the contents of the database. 278 | 279 | For the avoidance of doubt, this Section 4 supplements and does not 280 | replace Your obligations under this Public License where the Licensed 281 | Rights include other Copyright and Similar Rights. 282 | 283 | 284 | Section 5 -- Disclaimer of Warranties and Limitation of Liability. 285 | 286 | a. UNLESS OTHERWISE SEPARATELY UNDERTAKEN BY THE LICENSOR, TO THE 287 | EXTENT POSSIBLE, THE LICENSOR OFFERS THE LICENSED MATERIAL AS-IS 288 | AND AS-AVAILABLE, AND MAKES NO REPRESENTATIONS OR WARRANTIES OF 289 | ANY KIND CONCERNING THE LICENSED MATERIAL, WHETHER EXPRESS, 290 | IMPLIED, STATUTORY, OR OTHER. THIS INCLUDES, WITHOUT LIMITATION, 291 | WARRANTIES OF TITLE, MERCHANTABILITY, FITNESS FOR A PARTICULAR 292 | PURPOSE, NON-INFRINGEMENT, ABSENCE OF LATENT OR OTHER DEFECTS, 293 | ACCURACY, OR THE PRESENCE OR ABSENCE OF ERRORS, WHETHER OR NOT 294 | KNOWN OR DISCOVERABLE. WHERE DISCLAIMERS OF WARRANTIES ARE NOT 295 | ALLOWED IN FULL OR IN PART, THIS DISCLAIMER MAY NOT APPLY TO YOU. 296 | 297 | b. TO THE EXTENT POSSIBLE, IN NO EVENT WILL THE LICENSOR BE LIABLE 298 | TO YOU ON ANY LEGAL THEORY (INCLUDING, WITHOUT LIMITATION, 299 | NEGLIGENCE) OR OTHERWISE FOR ANY DIRECT, SPECIAL, INDIRECT, 300 | INCIDENTAL, CONSEQUENTIAL, PUNITIVE, EXEMPLARY, OR OTHER LOSSES, 301 | COSTS, EXPENSES, OR DAMAGES ARISING OUT OF THIS PUBLIC LICENSE OR 302 | USE OF THE LICENSED MATERIAL, EVEN IF THE LICENSOR HAS BEEN 303 | ADVISED OF THE POSSIBILITY OF SUCH LOSSES, COSTS, EXPENSES, OR 304 | DAMAGES. WHERE A LIMITATION OF LIABILITY IS NOT ALLOWED IN FULL OR 305 | IN PART, THIS LIMITATION MAY NOT APPLY TO YOU. 306 | 307 | c. The disclaimer of warranties and limitation of liability provided 308 | above shall be interpreted in a manner that, to the extent 309 | possible, most closely approximates an absolute disclaimer and 310 | waiver of all liability. 311 | 312 | 313 | Section 6 -- Term and Termination. 314 | 315 | a. This Public License applies for the term of the Copyright and 316 | Similar Rights licensed here. However, if You fail to comply with 317 | this Public License, then Your rights under this Public License 318 | terminate automatically. 319 | 320 | b. Where Your right to use the Licensed Material has terminated under 321 | Section 6(a), it reinstates: 322 | 323 | 1. automatically as of the date the violation is cured, provided 324 | it is cured within 30 days of Your discovery of the 325 | violation; or 326 | 327 | 2. upon express reinstatement by the Licensor. 328 | 329 | For the avoidance of doubt, this Section 6(b) does not affect any 330 | right the Licensor may have to seek remedies for Your violations 331 | of this Public License. 332 | 333 | c. For the avoidance of doubt, the Licensor may also offer the 334 | Licensed Material under separate terms or conditions or stop 335 | distributing the Licensed Material at any time; however, doing so 336 | will not terminate this Public License. 337 | 338 | d. Sections 1, 5, 6, 7, and 8 survive termination of this Public 339 | License. 340 | 341 | 342 | Section 7 -- Other Terms and Conditions. 343 | 344 | a. The Licensor shall not be bound by any additional or different 345 | terms or conditions communicated by You unless expressly agreed. 346 | 347 | b. Any arrangements, understandings, or agreements regarding the 348 | Licensed Material not stated herein are separate from and 349 | independent of the terms and conditions of this Public License. 350 | 351 | 352 | Section 8 -- Interpretation. 353 | 354 | a. For the avoidance of doubt, this Public License does not, and 355 | shall not be interpreted to, reduce, limit, restrict, or impose 356 | conditions on any use of the Licensed Material that could lawfully 357 | be made without permission under this Public License. 358 | 359 | b. To the extent possible, if any provision of this Public License is 360 | deemed unenforceable, it shall be automatically reformed to the 361 | minimum extent necessary to make it enforceable. If the provision 362 | cannot be reformed, it shall be severed from this Public License 363 | without affecting the enforceability of the remaining terms and 364 | conditions. 365 | 366 | c. No term or condition of this Public License will be waived and no 367 | failure to comply consented to unless expressly agreed to by the 368 | Licensor. 369 | 370 | d. Nothing in this Public License constitutes or may be interpreted 371 | as a limitation upon, or waiver of, any privileges and immunities 372 | that apply to the Licensor or You, including from the legal 373 | processes of any jurisdiction or authority. 374 | 375 | 376 | ======================================================================= 377 | 378 | Creative Commons is not a party to its public 379 | licenses. Notwithstanding, Creative Commons may elect to apply one of 380 | its public licenses to material it publishes and in those instances 381 | will be considered the “Licensor.” The text of the Creative Commons 382 | public licenses is dedicated to the public domain under the CC0 Public 383 | Domain Dedication. Except for the limited purpose of indicating that 384 | material is shared under a Creative Commons public license or as 385 | otherwise permitted by the Creative Commons policies published at 386 | creativecommons.org/policies, Creative Commons does not authorize the 387 | use of the trademark "Creative Commons" or any other trademark or logo 388 | of Creative Commons without its prior written consent including, 389 | without limitation, in connection with any unauthorized modifications 390 | to any of its public licenses or any other arrangements, 391 | understandings, or agreements concerning use of licensed material. For 392 | the avoidance of doubt, this paragraph does not form part of the 393 | public licenses. 394 | 395 | Creative Commons may be contacted at creativecommons.org. 396 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Software vs Data 2 | 3 | 4 | > The version of this document of 9 December 2016 has been published as: 5 | > 6 | > Katz DS, Niemeyer KE, Smith AM, Anderson WL, Boettiger C, Hinsen K, Hooft R, Hucka M, Lee A, Löffler F, Pollard T, Rios F. (2016) Software vs. data in the context of citation. PeerJ Preprints 4:e2630v1 https://doi.org/10.7287/peerj.preprints.2630v1 7 | 8 | 9 | Author/Editors: 10 | Daniel S. Katz, 11 | Kyle E. Niemeyer, 12 | Arfon M. Smith 13 | 14 | Additional Authors: 15 | William L. Anderson, Carl Boettiger, Konrad Hinsen, Rob Hooft, Mike Hucka, Allen Lee, Frank Löffler, Tom Pollard, Bernadette M. Randles, Fernando Rios 16 | 17 | 18 | This repository is intended to be used to discuss and document the differences between software and data in the context of citation in the research record. 19 | 20 | It has been created in the process of the FORCE11 Software Citation Working Group[FORCE11 Software Citation Working Group](#F11SCWG) 21 | writing the FORCE11 Software Citation Principles[Smith et al. 2016a](#F11SCWG-web), 22 | and then the editors submitting them to PeerJ Computer Science[Smith et al. 2016b](#F11SCWG-PeerJCS) 23 | and responding to reviewer comments. 24 | 25 | We start with the idea that software, while similar to data in terms of not traditionally having been cited in publications, is also different than data. For the purposes of this document, software is defined as programs that tell a computer which actions to perform. Software is made up of code, and might be in the form of packages, libraries, scripts, compiled code, proprietary packages, services, or any other form of instructions for the computer to interpret. Software also encompasses additional components such as comments, instructions, and other information necessary to run the software. In the context of research (e.g., in science), the term "data" usually refers to electronic records of observations made in the course of a research study ("raw data") or to information derived from such observations by some form of processing ("processed data"), as well as the output of simulation or modeling software ("simulated data"). In the following, we use the term "data" in this specific sense. 26 | 27 | The confusion about the distinction between software and data comes in part from the much wider sense that the term "data" has in computing and information science, where it refers to anything that can be processed by a computer. In that sense, software is just a special kind of data. 28 | 29 | 30 | The remainder of this document gives examples of these differences. 31 | 32 | If you want to add a new difference, please do via a pull request. Similarly, if you want to add a citation or add a new explanation, please also do this via a pull request. If you want to discuss a difference (for example, you don't think it's correct), please open a new issue or discuss via an existing issue. If you do add text in a pull request, also add yourself as an additional author in that same request, following the existing format and keeping the additional author list in alphabetic order by surname. (And add a comma after all authors but the last one.) 33 | 34 | --- 35 | 36 | ## Format of this document: 37 | 38 | ### Statement 39 | 40 | Explanation if needed, 41 | 42 | including or followed by: 43 | 44 | Evidence: Citations 45 | 46 | --- 47 | 48 | ## List of Differences 49 | 50 | ### Software is executable, data is not. 51 | 52 | A commonsense definition of software is that it is "a set of instructions that direct a computer to do a specific task"[Chun 2004](#chun2004). On the other hand, data is simply a collection of facts or measurements (real or simulated). In other words, software is functionally active, while data is passive. Of course, software (in form) can be considered data as well, especially to functional programmers familiar with LISP and other languages with homoiconicity[Kay 1969](#homoiconicity). However, from the point of view of conducting research with software, the main difference is that software is associated with action: knowledge creation, information transformation, visualization, etc. An action can be thought of a functional transformation between two states of data: a "before" (e.g., input files, parameter settings, unstructured or tacit information) to an "after" state (e.g., output files, transformed data, structured knowledge). That is, software generally performs a function upon something (e.g., software processes data), while data generally has a function performed upon it (e.g., data is processed by software). If we accept the definitions of software and data given at the beginning of this section, then (at least in scientific research), the difference between data and software can be summarized by the statement of [Matthews et al. 2010](#matthews2010): "we are more interested in what software *does* rather than what software *is*." 53 | 54 | 55 | ### Data provides evidence, software provides a tool. 56 | 57 | Software exists to perform a task, while data does not. Software is fundamentally a *logical* construct, while data is fundamentally an *empirical* observation. Software can be used to express or explain processes and concepts, oftentimes with data as input. These differences have important consequences for how each may be re-used in the future: software may be used by any researchers seeking to apply the same methods, data by any researchers seeking evidence about the same facts. 58 | 59 | 60 | ### Software is a creative work, scientific data are facts or observations. 61 | 62 | In particular, software is generally subject to copyright protection as a creative work that can continue to evolve over time, while scientific data is frequently considered outside the domain of copyright as it is comprised of _contextual_ facts about the world (you cannot copyright the height of Mt. Everest.) Major scientific data repositories (e.g. [Dryad](http://datadryad.org/), [figshare](https://figshare.com/)) automatically apply licenses suited to data that may not be suited to software. 63 | 64 | Evidence: Can I apply a Creative Commons license to software?[Creative Commons](#cc-software); Non-software licenses[Choose a License](#choosealicense) 65 | 66 | 67 | ### Software suffers from a different type of bit rot than data: It is frequently built to use other software, leading to complex dependencies, and these dependent software packages also frequently change. 68 | 69 | In general, software must be constantly maintained and updated in order to continue to function as both the hardware and software environments on which it depends change. Operating systems, software and system libraries, programming language toolchains and other compile-time and run-time dependencies all evolve as their respective maintainers and developers find and fix bugs, and as user requirements demand new features and capabilities. This is sometimes called "software rot"[Raymond 1996](#Software-rot) and other times called "bit rot." On the other hand, bit rot for data, or data degradation[Wikipedia](#data-degradation), is generally thought of as changes in the underlying hardware or storage media that holds the bits, or changes in the software capable of interpreting the data. This definition of bit rot also affects software since software is actually stored as a set of bits on a filesystem, but software bit rot is generally thought of as a higher level concern than data- or file-level bit rot. 70 | 71 | 72 | ### The lifetime of software is generally not as long as that of data. 73 | 74 | The lifetime of software can reach 20 years or more, especially for well-maintained projects. The life of software can end if the task it was supposed to do is not needed anymore, or if another software does it in a better way. Data, on the other hand, often represents the results of an experiment. It might become less interesting with time, but it cannot be replaced as it is connected to one particular experiment at that particular time. In this sense, software is replaceable (by other software), while data is usually not. 75 | 76 | A 1995 NRC Report _Preserving Scientific Data on Our Physical Universe_[NRC 1995](#NRC-preserving) 77 | provides the following recommendations regarding retention criteria and the appraisal process (p. 40): 78 | "As a general rule, all observational data that are nonredundant, 79 | useful, and documented well enough for most primary uses should be 80 | permanently maintained. Laboratory data sets are candidates for 81 | long-term preservation if there is no realistic chance of repeating 82 | the experiment, or if the cost and intellectual effort required to 83 | collect and validate the data were so great that the long-term 84 | retention is clearly justified. For both observational and 85 | experimental data, the following retention criteria should be used 86 | to determine whether a data set should be saved: uniqueness, adequacy 87 | of documentation (metadata), availability of hardware to read the data 88 | records, cost of replacement, and evaluation by peer review. Complete 89 | metadata should define the content, format or representation, 90 | structure, and context of a data set." 91 | 92 | While software is often replaced by newer software, computational models and data analyses can be important digital artifacts that should be preserved[Rollins et al. 2014](#cml-2014) along with datasets in order to properly verify or reproduce[Peng 2011](#peng-2011) published findings. Long-term preservation of the software used in computational science is a wicked problem as outlined in the final report from the _Preserving.exe: Toward a National Strategy for Preservation Software_ 2013 meeting[Preserving.exe 2013](#preserve-exe-2013). At that time, best practices to facilitate reproducibility of computational science involve archiving of the following, in durable, plaintext formats: 93 | 94 | 1. the software itself, in source code form in a trusted digital repository 95 | 2. structured or unstructured narrative documentation (e.g., the ODD protocol [Grimm 2013](#grimm-2013)) specifically covering key components of the software 96 | 3. descriptive provenance metadata on the software dependencies needed to compile and run the software as well as any input data dependencies 97 | 98 | though these practices may change as virtualization and containerization become more common. 99 | 100 | ### Additional Differences? 101 | 102 | ## References 103 | 104 | [Choose a License] Choose an open source license, "Non-software licenses," http://choosealicense.com/non-software/ Accessed: 2016-08-16. [↩](#choosealicense-footnote) 105 | 106 | [Chun 2004] W. H. K. Chun, "On software, or the persistence of visual knowledge," Grey Room, vol. 18, pp. 26–51, 2004. doi:10.1162/1526381043320741 [↩](#chun2004-footnote) 107 | 108 | [Creative Commons] Creative Commons, FAQ, "Can I apply a Creative Commons license to software?", https://wiki.creativecommons.org/index.php/Frequently_Asked_Questions#Can_I_apply_a_Creative_Commons_license_to_software.3F Accessed: 2016-08-16. [↩](#cc-software-footnote) 109 | 110 | [FORCE11 Software Citation Working Group] FORCE11 Software Citation Working Group, GitHub repository, https://github.com/force11/force11-scwg. Accessed: 2016-07-10. [↩](#F11SCWG-footnote) 111 | 112 | [Grimm et al. 2013] Volker Grimm, Gary Polhill, Julia Touza, Documenting Social Simulation Models: The ODD Protocol as a Standard. In _Simulating Social Complexity: A Handbook_, pp. 117-133, 2013. http://dx.doi.org/10.1007/978-3-540-93813-2_7 [↩](#grimm-2013-footnote) 113 | 114 | [Matthews et al. 2010] B. Matthews, A. Shaon, J. Bicarregui, and C. Jones, “A framework for software preservation,” International Journal of Digital Curation, vol. 5, no. 1, pp. 91–105, 2010. doi:10.2218/ijdc.v5i1.145 [↩](#matthews2010-footnote) 115 | 116 | [NRC 1995] National Research Council, Preserving Scientific Data on Our Physical Universe: A New Strategy for Archiving the Nation's Scientific Information Resources, 1995. http://www.nap.edu/catalog/4871.html [↩](#NRC-preserving-footnote) 117 | 118 | [Peng 2011] Roger D. Peng, Reproducible Research in Computational Science, Science, vol 334, issue 6060, pp. 1226-1227, 2011. http://dx.doi.org/10.1126/science.1213847 [↩](#peng-2011-footnote) 119 | 120 | [Preserving.exe 2013] Library of Congress, Preserving.exe: Toward a National Strategy for Software Preservation, 2013. http://www.digitalpreservation.gov/multimedia/documents/PreservingEXE_report_final101813.pdf [↩](#cml-2014-footnote) 121 | 122 | [Rollins et al. 2014] Nathan D. Rollins, C. Michael Barton, Sean Bergin, Marco A. Janssen, Allen Lee, A Computational Model Library for publishing model documentation and code, Environmental Modelling and Software, vol 61, pp. 59-64, 2014. http://dx.doi.org/10.1016/j.envsoft.2014.06.022 [↩](#cml-2014-footnote) 123 | 124 | [Smith et al. 2016a] A. M. Smith, D. S. Katz, K. E. Niemeyer, and FORCE11 Software 125 | Citation Working Group “Software Citation Principles,” FORCE2016 Website, https://www.force11.org/software-citation-principles, 2016. Accessed: 2016-07-10. [↩](#F11SCWG-web-footnote) 126 | 127 | [Smith et al. 2016b] A. M. Smith, D. S. Katz, K. E. Niemeyer, and FORCE11 Software Citation Working Group, “Software Citation Principles,” PeerJ Computer Science 2:e86, 2016. https://doi.org/10.7717/peerj-cs.86 [↩](#F11SCWG-PeerJCS-footnote) 128 | 129 | [Wikipedia] Wikipedia, “Data degradation”. https://en.wikipedia.org/wiki/Data_degradation Accessed: 2016-11-23. [↩](#data-degradation-footnote) 130 | 131 | [Kay 1969] Kay, A. C. The Reactive Engine. The University of Utah, AAI7003806, 1969. [↩](#homoiconicity-footnote) 132 | 133 | [Raymond 1996] Raymond, Eric S. The New Hacker's Dictionary. MIT Press, 1996. 134 | [↩](#Software-rot-footnote) 135 | 136 | -------------------------------------------------------------------------------- /preprint/.gitignore: -------------------------------------------------------------------------------- 1 | # Common LaTeX things. 2 | *.aux 3 | *.glo 4 | *.idx 5 | *.log 6 | *.toc 7 | *.ist 8 | *.acn 9 | *.acr 10 | *.alg 11 | *.bbl 12 | *.blg 13 | *.dvi 14 | *.glg 15 | *.gls 16 | *.ilg 17 | *.ind 18 | *.lof 19 | *.lot 20 | *.maf 21 | *.mtc 22 | *.mtc1 23 | *.out 24 | *.synctex.gz 25 | 26 | # Common Emacs things. 27 | auto 28 | *~ 29 | .git/COMMIT_EDITMSG 30 | -------------------------------------------------------------------------------- /preprint/preprint.bib: -------------------------------------------------------------------------------- 1 | 2 | @article{SWCP, 3 | title = {Software citation principles}, 4 | author = {Smith, Arfon M. and Katz, Daniel S. and Niemeyer, Kyle E. and {FORCE11 Software Citation Working Group}}, 5 | year = 2016, 6 | month = sep, 7 | keywords = {Software citation, Software credit, Attribution}, 8 | abstract = { 9 | Software is a critical part of modern research and yet there is little support across the scholarly ecosystem for its acknowledgement and citation. Inspired by the activities of the FORCE11 working group focused on data citation, this document summarizes the recommendations of the FORCE11 Software Citation Working Group and its activities between June 2015 and April 2016. Based on a review of existing community practices, the goal of the working group was to produce a consolidated set of citation principles that may encourage broad adoption of a consistent policy for software citation across disciplines and venues. Our work is presented here as a set of software citation principles, a discussion of the motivations for developing the principles, reviews of existing community practice, and a discussion of the requirements these principles would place upon different stakeholders. Working examples and possible technical solutions for how these principles can be implemented will be discussed in a separate paper. 10 | }, 11 | volume = 2, 12 | pages = {e86}, 13 | journal = {PeerJ Computer Science}, 14 | issn = {2376-5992}, 15 | url = {https://doi.org/10.7717/peerj-cs.86}, 16 | doi = {10.7717/peerj-cs.86}, 17 | note={DOI: \href{https://doi.org/10.7717/peerj-cs.86}{10.7717/peerj-cs.86}} 18 | } 19 | 20 | @misc{SWCP-web, 21 | author = {Smith, Arfon M. and Katz, Daniel S. and Niemeyer, Kyle E. and {FORCE11 Software Citation Working Group}}, 22 | year = 2016, 23 | title = {Software citation principles}, 24 | note={URL: \url{https://www.force11.org/software-citation-principles} [Accessed: 2016-12-05]}, 25 | } 26 | 27 | @misc{F11-SCWG-repo, 28 | year = 2016, 29 | author = {{FORCE11 Software Citation Working Group}}, 30 | title = {{FORCE11} Software Citation Working Group {GitHub} Repository}, 31 | note={URL: \url{https://github.com/force11/force11-scwg} [Accessed: 2016-12-05]}, 32 | } 33 | 34 | @misc{this-repo, 35 | year = 2016, 36 | author = {Daniel S. Katz and Kyle E. Niemeyer and Arfon M. Smith and William L. Anderson and Carl Boettiger and Konrad Hinsen and Mike Hucka and Allen Lee and Frank L\"offler and Tom Pollard and Fernando Rios}, 37 | title = {Software vs. Data {GitHub} Repository}, 38 | note={URL: \url{https://github.com/danielskatz/software-vs-data} [Accessed: 2016-12-05]}, 39 | } 40 | 41 | 42 | @article{Chun2004, 43 | Author = {Chun, Wendy Hui Kyong}, 44 | Journal = {Grey Room}, 45 | Month = {2016/12/05}, 46 | Pages = {26--51}, 47 | Title = {On Software, or the Persistence of Visual Knowledge}, 48 | Year = {2005}, 49 | note={DOI:\href{http://dx.doi.org/10.1162/1526381043320741}{10.1162/1526381043320741}}, 50 | Publisher = {MIT Press}, 51 | } 52 | 53 | @article{Matthews2010, 54 | author={B. Matthews and A. Shaon and J. Bicarregui and C. Jones}, 55 | title={A framework for software preservation}, 56 | journal={International Journal of Digital Curation}, 57 | volume={5}, 58 | number={1}, 59 | pages={91?105}, 60 | year={2010}, 61 | note={DOI:\href{http://dx.doi.org/10.2218/ijdc.v5i1.145}{10.2218/ijdc.v5i1.145}}, 62 | } 63 | 64 | @misc{choose-a-license, 65 | author = {{Choose an open source license}}, 66 | year=2016, 67 | title = {Non-software licenses}, 68 | note={URL: \url{http://choosealicense.com/non-software/} [Accessed: 2016-12-05]}, 69 | } 70 | 71 | @misc{CC-license, 72 | author = {{Creative Commons}}, 73 | year=2016, 74 | title = {Can I apply a Creative Commons license to software?}, 75 | note={URL: \url{https://wiki.creativecommons.org/index.php/Frequently_Asked_Questions#Can_I_apply_a_Creative_Commons_license_to_software.3F} [Accessed: 2016-12-05]}, 76 | } 77 | 78 | @book{Raymond1996, 79 | title={The New Hacker's Dictionary}, 80 | author={Raymond, Eric S}, 81 | year={1996}, 82 | publisher={MIT Press} 83 | } 84 | 85 | @misc{wiki-data-degredation, 86 | author = {{Wikipedia}}, 87 | year=2016, 88 | title = {Data degradation}, 89 | note={URL: \url{https://en.wikipedia.org/wiki/Data_degradation} [Accessed: 2016-12-05]}, 90 | } 91 | 92 | @phdthesis{Kay1969, 93 | author = {Kay, Alan Curtis}, 94 | title = {The Reactive Engine}, 95 | year = {1969}, 96 | note = {AAI7003806}, 97 | school = {The University of Utah}, 98 | } 99 | 100 | 101 | 102 | @book{NRC1995, 103 | author={{National Research Council}}, 104 | title={Preserving Scientific Data on Our Physical Universe: A New Strategy for Archiving the Nation's Scientific Information Resources}, 105 | year=1995, 106 | publisher={National Academies Press}, 107 | note={URL: \url{http://www.nap.edu/catalog/4871.html} [Accessed: 2016-12-05]}, 108 | } 109 | 110 | @article{Rollins2014, 111 | title = "A Computational Model Library for publishing model documentation and code ", 112 | journal = "Environmental Modelling \& Software ", 113 | volume = "61", 114 | number = "", 115 | pages = "59 - 64", 116 | year = "2014", 117 | note={DOI:\href{http://dx.doi.org/10.1016/j.envsoft.2014.06.022}{10.1016/j.envsoft.2014.06.022}}, 118 | doi = "http://dx.doi.org/10.1016/j.envsoft.2014.06.022", 119 | url = "http://www.sciencedirect.com/science/article/pii/S1364815214001959", 120 | author = "Nathan D. Rollins and C. Michael Barton and Sean Bergin and Marco A. Janssen and Allen Lee", 121 | } 122 | 123 | @article {Peng2011, 124 | author = {Peng, Roger D.}, 125 | title = {Reproducible Research in Computational Science}, 126 | volume = {334}, 127 | number = {6060}, 128 | pages = {1226--1227}, 129 | year = {2011}, 130 | doi = {10.1126/science.1213847}, 131 | publisher = {American Association for the Advancement of Science}, 132 | issn = {0036-8075}, 133 | URL = {http://science.sciencemag.org/content/334/6060/1226}, 134 | eprint = {http://science.sciencemag.org/content/334/6060/1226.full.pdf}, 135 | journal = {Science}, 136 | note={DOI:\href{http://dx.doi.org/10.1126/science.1213847}{10.1126/science.1213847}}, 137 | } 138 | 139 | 140 | @misc{Preserving.exe, 141 | author={{Library of Congress}}, 142 | title={Preserving.exe: Toward a National Strategy for Software Preservation}, 143 | year=2013, 144 | note={URL: \url{http://www.digitalpreservation.gov/multimedia/documents/PreservingEXE_report_final101813.pdf} [Accessed: 2016-12-05]}, 145 | } 146 | 147 | 148 | @Incollection{Grimm2013, 149 | author="Grimm, Volker 150 | and Polhill, Gary 151 | and Touza, Julia", 152 | title="Documenting Social Simulation Models: The {ODD} Protocol as a Standard", 153 | year="2013", 154 | pages="117--133", 155 | isbn="978-3-540-93813-2", 156 | doi="10.1007/978-3-540-93813-2_7", 157 | url="http://dx.doi.org/10.1007/978-3-540-93813-2_7", 158 | publisher="Springer Berlin Heidelberg", 159 | note={DOI:\href{http://dx.doi.org/10.1007/978-3-540-93813-2_7}{10.1007/978-3-540-93813-2\_7}}, 160 | crossref={SSC}, 161 | } 162 | 163 | @book{SSC, 164 | title = {AI Game Programming Wisdom 2}, 165 | bookTitle="Simulating Social Complexity: A Handbook", 166 | publisher="Springer Berlin Heidelberg", 167 | year="2013", 168 | editor="Edmonds, Bruce 169 | and Meyer, Ruth", 170 | address="Berlin, Heidelberg", 171 | } 172 | 173 | @article{WSSSPE2, 174 | Author = {Daniel S. Katz and Sou-Cheng T. Choi and Nancy Wilkins-Diehr and Neil {Chue Hong} and Colin C. Venters and James Howison and Frank J. Seinstra and Matthew Jones and Karen Cranston and Thomas L. Clune and Miguel de Val{-}Borro and Richard Littauer}, 175 | Journal = {Journal Open Research Software}, 176 | Number = {1}, 177 | Pages = {e7}, 178 | Title = {Report on the Second Workshop on Sustainable Software for Science: Practice and Experiences {(WSSSPE2)}}, 179 | Volume = {4}, 180 | Year = {2016}, 181 | doi = {10.5334/jors.85}, 182 | note={DOI:\href{http://dx.doi.org/10.5334/jors.85}{10.5334/jors.85}}, 183 | } 184 | 185 | -------------------------------------------------------------------------------- /preprint/preprint.tex: -------------------------------------------------------------------------------- 1 | %% Submissions for peer-review must enable line-numbering 2 | %% using the lineno option in the \documentclass command. 3 | %% 4 | %% Preprints and camera-ready submissions do not need 5 | %% line numbers, and should have this option removed. 6 | %% 7 | %% Please note that the line numbering option requires 8 | %% version 1.1 or newer of the wlpeerj.cls file, and 9 | %% the corresponding author info requires v1.2 10 | 11 | % \documentclass[fleqn,10pt,lineno]{wlpeerj} % for journal submissions 12 | \documentclass[fleqn,10pt]{wlpeerj} % for preprint submissions 13 | 14 | \usepackage{hyperref} 15 | 16 | \title{Software vs.\ data in the context of citation} 17 | 18 | \author[1]{Daniel~S.~Katz} 19 | \author[2]{Kyle~E.~Niemeyer} 20 | \author[3]{Arfon~M.~Smith} 21 | \author[4]{William~L.~Anderson} 22 | \author[5]{Carl~Boettiger} 23 | \author[6]{Konrad~Hinsen} 24 | \author[7]{Rob~Hooft} 25 | \author[8]{Michael~Hucka} 26 | \author[9]{Allen~Lee} 27 | \author[10]{Frank~L\"offler} 28 | \author[11]{Tom~Pollard} 29 | \author[12]{Bernadette~M.~Randles} 30 | \author[13]{Fernando~Rios} 31 | \affil[1]{National Center for Supercomputing Applications \& Electrical and Computer Engineering Department \& School of Information Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois, USA; d.katz@ieee.org; ORCID: 0000-0001-5934-7525} 32 | \affil[2]{School of Mechanical, Industrial, and Manufacturing Engineering, Oregon State University, Corvallis, Oregon, USA; kyle.niemeyer@oregonstate.edu; ORCID: 0000-0003-4425-7097} 33 | \affil[3]{Space Telescope Science Institute, Baltimore, Maryland, USA; arfon@stsci.edu; ORCID: 0000-0002-3957-2474} 34 | \affil[4]{School of Information, University of Texas at Austin, Austin, Texas, USA; band@acm.org; ORCID: 0000-0003-3200-7947} 35 | \affil[5]{Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA; cboettig@berkeley.edu; ORCID: 0000-0002-1642-628X} 36 | \affil[6]{Centre de Biophysique Mol\'{e}culaire (CNRS), Orl\'{e}ans, France; konrad.hinsen@cnrs.fr; ORCID: 0000-0003-0330-9428} 37 | \affil[7]{Dutch Techcentre for Life Sciences; Utrecht, The Netherlands; rob.hooft@dtls.nl; ORCID: 0000-0001-6825-9439} 38 | \affil[8]{Computing and Mathematical Sciences, California Institute of Technology, Pasadena, California, USA; mhucka@caltech.edu; ORCID: 0000-0001-9105-5960} 39 | \affil[9]{Center for Behavior, Institutions \& the Environment, Biosocial Complexity Initiative, Arizona State University, Tempe, Arizona, USA; allen.lee@asu.edu; ORCID: 0000-0002-6523-6079} 40 | \affil[10]{Center for Computation \& Technology, Louisiana State University, Baton Rouge, Louisiana, USA; knarf@cct.lsu.edu; ORCID: 0000-0001-6643-6323} 41 | \affil[11]{Institute for Medical Engineering \& Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; tpollard@mit.edu; ORCID: 0000-0002-5676-7898} 42 | \affil[12]{Department of Information Studies, University of California, Los Angeles, California, USA; randles@ucla.edu; ORCID: 0000-0002-9533-3531} 43 | \affil[13]{Data Management Services, The Sheridan Libraries, Johns Hopkins University, Baltimore, Maryland, USA; rios@jhu.edu; ORCID: 0000-0001-6262-3260} 44 | \corrauthor[1]{Daniel S. Katz}{d.katz@ieee.org} 45 | 46 | 47 | % \keywords{Keyword1, Keyword2, Keyword3} 48 | 49 | \begin{abstract} 50 | Software is data, but it is not just data. While ``data'' in computing and information science can refer to anything that can be processed by a computer, software is a special kind of data that can be a creative, executable tool that operates on data. However, software and data are similar in that they both traditionally have not been cited in publications. This paper discusses the differences between software and data in the context of citation, by providing examples and referring to evidence in the form of citations. 51 | \end{abstract} 52 | 53 | \begin{document} 54 | 55 | \flushbottom 56 | \maketitle 57 | \thispagestyle{empty} 58 | 59 | \section*{Introduction} 60 | 61 | This preprint is a snapshot of the GitHub repository~\citep{this-repo}. The repository is intended to be used to discuss and document the differences between software and data in the context of citation in the research record. This preprint allows the current state of this work to be cited. 62 | 63 | The repository was created as part of the FORCE11 Software Citation Working Group~\citep{F11-SCWG-repo} writing the FORCE11 Software Citation Principles~\citep{SWCP-web}, and then the editors submitting them to PeerJ Computer Science~\citep{SWCP} and responding to reviewer comments. 64 | 65 | We start with the idea that software, while similar to data in terms of not traditionally having been cited in publications, is also different than data. For the purposes of this document, software is defined as programs that tell a computer which actions to perform. Software is made up of code, and might be in the form of packages, libraries, scripts, compiled code, proprietary packages, services, or any other form of instructions for the computer to interpret. Software also encompasses additional components such as comments, instructions, and other information necessary to run the software. In the context of research (e.g., in science), the term ``data'' usually refers to electronic records of observations made in the course of a research study (``raw data'') or to information derived from such observations by some form of processing (``processed data''), as well as the output of simulation or modeling software (``simulated data''). In the following, we use the term ``data'' in this specific sense. 66 | 67 | The confusion about the distinction between software and data comes in part from the much wider sense that the term ``data'' has in computing and information science, where it refers to anything that can be processed by a computer. In that sense, software is just a special kind of data. 68 | 69 | The remainder of this document gives examples of these differences. The format of this document is a series of statements (as subsections), each with an explanation, including or followed by evidence in the form of citations. 70 | 71 | \subsection*{Updating this document} 72 | 73 | To add a new difference between software and other forms of data, please submit a pull request in the repository~\citep{this-repo}. Similarly, to add or update a citation or to add a new explanation, please also do this via a pull request. To discuss a difference (for example, you don't think it is correct), please open a new issue or discuss via an existing issue, again in the repository~\citep{this-repo}. If you do add text in a pull request, also add yourself as an additional author in that same request. Once there is a significant set of changes, this preprint will be updated. 74 | 75 | 76 | 77 | \section*{List of Differences} 78 | \label{sec:differences} 79 | 80 | \subsection*{Software is executable, data is not} 81 | 82 | A commonsense definition of software is that it is ``a set of instructions that direct a computer to do a specific task''~\citep{Chun2004}. On the other hand, data is simply a collection of facts or measurements (real or simulated). In other words, software is functionally active, while data is passive. Of course, software (in form) can be considered data as well, especially to functional programmers familiar with LISP and other languages with homoiconicity~\citep{Kay1969}. However, from the point of view of conducting research with software, the main difference is that software is associated with action: knowledge creation, information transformation, visualization, etc. An action can be thought of a functional transformation between two states of data: a ``before'' (e.g., input files, parameter settings, unstructured or tacit information) to an ``after'' state (e.g., output files, transformed data, structured knowledge). That is, software generally performs a function upon something (e.g., software processes data), while data generally has a function performed upon it (e.g., data is processed by software). If we accept the definitions of software and data given at the beginning of this section, then (at least in scientific research), the difference between data and software can be summarized by the statement of \cite{Matthews2010}: ``we are more interested in what software does rather than what software is.'' 83 | 84 | \subsection*{Data provides evidence, software provides a tool} 85 | 86 | Software exists to perform a task, while data does not. Software is fundamentally a logical construct, while data is fundamentally an empirical observation. Software can be used to express or explain processes and concepts, oftentimes with data as input. These differences have important consequences for how each may be re-used in the future: software may be used by any researchers seeking to apply the same methods, data by any researchers seeking evidence about the same facts. 87 | 88 | \subsection*{Software is a creative work, scientific data are facts or observations} 89 | 90 | In particular, software is generally subject to copyright protection as a creative work that can continue to evolve over time, while scientific data is frequently considered outside the domain of copyright as it is comprised of contextual facts about the world (you cannot copyright the height of Mt. Everest.) Major scientific data repositories (e.g., Dryad, figshare) automatically apply licenses suited to data that may not be suited to software. 91 | 92 | Evidence: Can I apply a Creative Commons license to software?~\citep{CC-license}; Non-software licenses~\citep{choose-a-license} 93 | 94 | \subsection*{Software suffers from a different type of bit rot than data: It is frequently built to use other software, leading to complex dependencies, and these dependent software packages also frequently change} 95 | 96 | In general, software must be constantly maintained and updated in order to continue to function as both the hardware and software environments on which it depends change. Operating systems, software and system libraries, programming language toolchains and other compile-time and run-time dependencies all evolve as their respective maintainers and developers find and fix bugs, and as user requirements demand new features and capabilities. This is sometimes called ``software rot''~\citep{Raymond1996} and other times called ``bit rot.'' On the other hand, bit rot for data, or data degradation~\citep{wiki-data-degredation}, is generally thought of as changes in the underlying hardware or storage media that holds the bits, or changes in the software capable of interpreting the data. This definition of bit rot also affects software since software is actually stored as a set of bits on a filesystem, but software bit rot is generally thought of as a higher level concern than data- or file-level bit rot. 97 | 98 | \subsection*{The lifetime of software is generally not as long as that of data} 99 | 100 | The lifetime of software can reach 20 years or more, especially for well-maintained projects. The life of software can end if the task it was supposed to do is not needed anymore, or if another software does it in a better way. Data, on the other hand, often represents the results of an experiment. It might become less interesting with time, but it cannot be replaced as it is connected to one particular experiment at that particular time. In this sense, software is replaceable (by other software), while data is usually not. 101 | 102 | A 1995 NRC Report Preserving Scientific Data on Our Physical Universe~\citep{NRC1995} provides the following recommendations regarding retention criteria and the appraisal process (p. 40): ``As a general rule, all observational data that are nonredundant, useful, and documented well enough for most primary uses should be permanently maintained. Laboratory data sets are candidates for long-term preservation if there is no realistic chance of repeating the experiment, or if the cost and intellectual effort required to collect and validate the data were so great that the long-term retention is clearly justified. For both observational and experimental data, the following retention criteria should be used to determine whether a data set should be saved: uniqueness, adequacy of documentation (metadata), availability of hardware to read the data records, cost of replacement, and evaluation by peer review. Complete metadata should define the content, format or representation, structure, and context of a data set.'' 103 | 104 | While software is often replaced by newer software, computational models and data analyses can be important digital artifacts that should be preserved~\citep{rollins2014} along with datasets in order to properly verify or reproduce~\citep{Peng2011} published findings. Long-term preservation of the software used in computational science is a wicked problem as outlined in the final report from the Preserving.exe: Toward a National Strategy for Preservation Software 2013 meeting~\citep{Preserving.exe}. At that time, best practices to facilitate reproducibility of computational science involve archiving of the following, in durable, plaintext formats: 105 | \begin{enumerate} 106 | \item the software itself, in source code form in a trusted digital repository 107 | \item structured or unstructured narrative documentation (e.g., the ODD protocol~\citep{Grimm2013}) specifically covering key components of the software 108 | \item descriptive provenance metadata on the software dependencies needed to compile and run the software as well as any input data dependencies 109 | \end{enumerate} 110 | though these practices may change as virtualization and containerization become more common. 111 | 112 | \section*{Acknowledgments} 113 | 114 | The initial version of the text in this document was a list in an early version of \citep{SWCP}, which was developed by the FORCE11 Software Citation Working Group. The members of this working group were an initial set of volunteers who were joined by members of a related WSSSPE2 working group~\citep{WSSSPE2}. During 115 | the review process, it became clear having this text in that document was a distraction for the reviewers, 116 | so it was extracted into a repository~\citep{this-repo} where it continued to develop. As such, 117 | both FORCE11 (The Future of Research Communication and eScholarship; \url{https://www.force11.org}) and WSSSPE (Working towards Sustainable Software for Science: Practice and Experiences; \url{http://wssspe.researchcomputing.org.uk}) are acknowledged as instigating this discussion. 118 | 119 | \bibliography{preprint} 120 | 121 | \end{document} 122 | -------------------------------------------------------------------------------- /preprint/wlpeerj.cls: -------------------------------------------------------------------------------- 1 | % 2 | % An unofficial LaTeX class for PeerJ articles. 3 | % 4 | % Created by Overleaf (writeLaTeX). 5 | % 6 | % Based on the SelfArx document class. 7 | % 8 | \NeedsTeXFormat{LaTeX2e} 9 | \ProvidesClass{wlpeerj}[18/08/2016, v1.2] 10 | \RequirePackage[utf8]{inputenc} 11 | \RequirePackage[english]{babel} 12 | 13 | \RequirePackage{ifthen} 14 | \RequirePackage{calc} 15 | \AtEndOfClass{\RequirePackage{microtype}} 16 | \newif\if@peerjlineno 17 | \DeclareOption{lineno}{\@peerjlinenotrue} 18 | \DeclareOption*{\PassOptionsToClass{\CurrentOption}{article}} 19 | \ProcessOptions* 20 | \LoadClass{article} 21 | \RequirePackage{times} % Loads the Times-Roman Fonts 22 | \RequirePackage{mathptmx} % Loads the Times-Roman Math Fonts 23 | \RequirePackage{lineno} % For numbering the lines if lineno option is given 24 | \if@peerjlineno\linenumbers\fi 25 | 26 | \RequirePackage{ifpdf} 27 | 28 | \RequirePackage{amsmath,amsfonts,amssymb} 29 | \RequirePackage{graphicx,xcolor} 30 | \RequirePackage{booktabs} 31 | \RequirePackage{authblk} 32 | 33 | \RequirePackage[left=5cm,% 34 | right=2cm,% 35 | top=2.25cm,% 36 | bottom=2.25cm,% 37 | headheight=12pt,% 38 | letterpaper]{geometry}% 39 | 40 | \RequirePackage[labelfont={bf,sf},% 41 | labelsep=period,% 42 | justification=raggedright]{caption} 43 | 44 | \RequirePackage{natbib} 45 | \bibliographystyle{apalike} 46 | 47 | % 48 | % writeLaTeX logo 49 | % 50 | \newcommand\wllogo{% 51 | \renewcommand*\rmdefault{ugq}\normalfont\upshape{}write% 52 | \renewcommand*\rmdefault{cmr}\normalfont\upshape{\bf\LaTeX}} 53 | 54 | % 55 | % headers and footers 56 | % 57 | \RequirePackage{fancyhdr} % custom headers/footers 58 | \RequirePackage{lastpage} % Number of pages in the document 59 | \pagestyle{fancy} % Enables the custom headers/footers 60 | % Headers 61 | \lhead{}% 62 | \chead{}% 63 | \rhead{}% 64 | % Footers 65 | \lfoot{}% 66 | \cfoot{}% 67 | \rfoot{\small\sffamily\bfseries\thepage/\pageref{LastPage}}% 68 | \renewcommand{\headrulewidth}{0pt}% % No header rule 69 | \renewcommand{\footrulewidth}{0pt}% % No footer rule 70 | 71 | % 72 | % section/subsection/paragraph set-up 73 | % 74 | \RequirePackage[explicit]{titlesec} 75 | \titleformat{\section} 76 | {\color{color1}\large\sffamily\bfseries} 77 | {\thesection} 78 | {0.5em} 79 | {\MakeUppercase{#1}} 80 | [] 81 | \titleformat{name=\section,numberless} 82 | {\color{color1}\large\sffamily\bfseries} 83 | {} 84 | {0em} 85 | {\MakeUppercase{#1}} 86 | [] 87 | \titleformat{\subsection} 88 | {\sffamily\bfseries} 89 | {\thesubsection} 90 | {0.5em} 91 | {#1} 92 | [] 93 | \titleformat{\subsubsection} 94 | {\sffamily\small\bfseries\itshape} 95 | {\thesubsubsection} 96 | {0.5em} 97 | {#1} 98 | [] 99 | \titleformat{\paragraph}[runin] 100 | {\sffamily\small\bfseries} 101 | {} 102 | {0em} 103 | {#1} 104 | \titlespacing*{\section}{0pc}{3ex \@plus4pt \@minus3pt}{5pt} 105 | \titlespacing*{\subsection}{0pc}{2.5ex \@plus3pt \@minus2pt}{0pt} 106 | \titlespacing*{\subsubsection}{0pc}{2ex \@plus2.5pt \@minus1.5pt}{0pt} 107 | \titlespacing*{\paragraph}{0pc}{1.5ex \@plus2pt \@minus1pt}{10pt} 108 | 109 | % 110 | % tableofcontents set-up 111 | % 112 | \usepackage{titletoc} 113 | \contentsmargin{0cm} 114 | \titlecontents{section}[\tocsep] 115 | {\addvspace{4pt}\small\bfseries\sffamily} 116 | {\contentslabel[\thecontentslabel]{\tocsep}} 117 | {} 118 | {\hfill\thecontentspage} 119 | [] 120 | \titlecontents{subsection}[\tocsep] 121 | {\addvspace{2pt}\small\sffamily} 122 | {\contentslabel[\thecontentslabel]{\tocsep}} 123 | {} 124 | {\ \titlerule*[.5pc]{.}\ \thecontentspage} 125 | [] 126 | \titlecontents*{subsubsection}[\tocsep] 127 | {\footnotesize\sffamily} 128 | {} 129 | {} 130 | {} 131 | [\ \textbullet\ ] 132 | 133 | \RequirePackage{enumitem} 134 | %\setlist{nolistsep} % Uncomment to remove spacing between items in lists (enumerate, itemize) 135 | 136 | % Remove brackets from numbering in List of References 137 | \renewcommand{\@biblabel}[1]{\bfseries\color{color1}\textsuperscript{[#1]}} 138 | 139 | % 140 | % article meta data 141 | %% LLT 18 Aug 2016: no more! 142 | % \newcommand{\keywords}[1]{\def\@keywords{#1}} 143 | %% LLT 18 Aug 2016: but need corresponding author 144 | \newcommand{\corrauthor}[3][]{% 145 | \def\thecorrauthor{% 146 | Corresponding author:\par #2$^{#1}$\par 147 | \medskip 148 | Email address: #3\par} 149 | } 150 | 151 | \def\xabstract{abstract} 152 | \long\def\abstract#1\end#2{\def\two{#2}\ifx\two\xabstract 153 | \long\gdef\theabstract{\ignorespaces#1} 154 | \def\go{\end{abstract}}\else 155 | \typeout{^^J^^J PLEASE DO NOT USE ANY \string\begin\space \string\end^^J 156 | COMMANDS WITHIN ABSTRACT^^J^^J}#1\end{#2} 157 | \gdef\theabstract{\vskip12pt BADLY FORMED ABSTRACT: PLEASE DO 158 | NOT USE {\tt\string\begin...\string\end} COMMANDS WITHIN 159 | THE ABSTRACT\vskip12pt}\let\go\relax\fi 160 | \go} 161 | 162 | % 163 | % custom title page 164 | % 165 | \renewcommand{\@maketitle}{% 166 | {% 167 | \thispagestyle{empty}% 168 | \vskip-36pt% 169 | {\raggedright\sffamily\bfseries\fontsize{20}{25}\selectfont \@title\par}% 170 | \vskip10pt 171 | {\raggedright\sffamily\fontsize{12}{16}\selectfont \@author\par} 172 | \vskip1em% 173 | % LLT 18 Aug 2016: needs corresponding author now 174 | \ifdefined\thecorrauthor 175 | {\raggedright\sffamily\thecorrauthor\par} 176 | \fi 177 | \vskip18pt 178 | {% 179 | \noindent 180 | {\parbox{\dimexpr\linewidth-2\fboxsep\relax}{\color{color1}\large\sffamily\textbf{ABSTRACT}}} 181 | }% 182 | \vskip10pt\nolinenumbers 183 | {% 184 | \noindent 185 | \colorbox{color2}{% 186 | \parbox{\dimexpr\linewidth-2\fboxsep\relax}{% 187 | \sffamily\small\vskip1ex\if@peerjlineno\internallinenumbers\fi\theabstract 188 | }% 189 | }% 190 | %% LLT 18 Aug 2016: no more keywords 191 | % \vskip18pt% 192 | % \noindent 193 | % \parbox{\dimexpr\linewidth-2\fboxsep\relax}{% 194 | % \if@peerjlineno\internallinenumbers\fi% 195 | % {\color{color1}\keywordname\hspace*{1em}} \@keywords% 196 | % }% 197 | }% 198 | \vskip25pt% 199 | }% 200 | }% 201 | %----------------------------------------------- 202 | \setlength{\columnsep}{0.55cm} % Distance between the two columns of text 203 | \setlength{\fboxrule}{0.75pt} % Width of the border around the abstract 204 | 205 | \definecolor{color1}{RGB}{0,0,0} % Color of section headings 206 | \definecolor{color2}{RGB}{250,232,207} % Color of the box behind the abstract 207 | \newcommand{\keywordname}{Keywords:} % Defines the keywords heading name 208 | 209 | \renewcommand\Authfont{\fontsize{12}{14}\usefont{OT1}{phv}{b}{n}} 210 | \renewcommand\Affilfont{\fontsize{10}{12}\usefont{OT1}{phv}{b}{n}} 211 | 212 | \newlength{\tocsep} 213 | \setlength\tocsep{1.5pc} % Sets the indentation of the sections in the table of contents 214 | \setcounter{tocdepth}{3} % Show only three levels in the table of contents section: sections, subsections and subsubsections 215 | 216 | \usepackage{lipsum} % Required to insert dummy text 217 | %----------------------------------------------- 218 | \let\oldbibliography\thebibliography 219 | \renewcommand{\thebibliography}[1]{% 220 | \addcontentsline{toc}{section}{\hspace*{-\tocsep}\refname}% 221 | \oldbibliography{#1}% 222 | \setlength\itemsep{0pt}% 223 | } --------------------------------------------------------------------------------