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2 results for “khipu”
The Open Khipu Repository
<p><strong>Release v2.0.0 changes:</strong></p> <p>Implements the khipu renaming procedure described in Brezine, Clindaniel, Ghezzi, Hyland and Medrano (Under Review) "A New Naming Convention for Andean Khipus" (see replication code here: https://doi.org/10.5281/zenodo.6908292).</p> <p>Note that as a part of this release, we dropped several duplicate khipu recordings and implemented a more neutral "KH"-based naming scheme in a new <code>okr_num</code> field in the <code>khipu_main</code> table (see replication code linked above for more detail).</p> <p><strong>Description of Repository</strong></p> <p>This open-source digital repository stores the most up-to-date data and metadata on extant Inka-style khipus from archaeological sites in the Andes, as well as museums around the world. Inka khipus were unique pre-Columbian, Andean recording devices that used three-dimensional signs -- primarily knots, cords, and colors -- as symbols functionally akin to those of early writing systems in other cultures. Spanish chronicles, as well as contemporary khipu studies indicate that the Inka used khipus to record everything from accounting records to historical narratives. The khipu recording system remains undeciphered, however. The purpose of this repository is to enable computational khipu research and Inka khipu decipherment efforts.</p> <p>Currently, data is stored in a serverless SQLite relational database (khipu.db) that contains all known khipu data recorded and published by Inka khipu scholars. A list of known contributors is available <a href="https://github.com/khipulab/open-khipu-repository/blob/master/contributors">here</a> in the repository. If you have recorded khipu data in the database, but are not listed, please contact us (<a href="mailto:okr-team@googlegroups.com">okr-team@googlegroups.com</a>).</p> <p>The data in this repository will continue to be updated as more is learned about khipus and additional khipus become available for study. All new releases and changes to the repository are overseen by the Open Khipu Repository Advisory Board (<a href="mailto:okr-team@googlegroups.com">okr-team@googlegroups.com</a>), currently consisting of Carrie Brezine, Mackinley FitzPatrick, Iván Ghezzi, Sabine Hyland, Manuel Medrano, and Jeffrey Splitstoser. The repository is administered by the Open Khipu Research Laboratory, under the direction of Mackinley FitzPatrick (<a href="mailto:mackfitzpatrick@fas.harvard.edu">mackfitzpatrick@fas.harvard.edu</a>).</p> <p>A part of the OKR Advisory Board's mission is to positively influence the field of khipu studies in ways that are inclusive and respectful of all interested scholars. We recognize that the data in the OKR were not collected in a vacuum. The existence of the OKR is a result of power structures within the global discipline of Anthropology and of academia more generally. The data compiled here reflect funding disparities between scholars at different levels and between institutions in different countries. They reflect geographic privilege and economic privilege, for instance in scholars' disparate access to travel. The OKR is itself one artifact of colonialist Archaeology and Anthropology as practiced by North American and European scholars. It is also a product of unfortunate linguistic distancing -- we are well aware that native speakers of Andean languages have so far had little involvement in collecting the data in the OKR. We hope to change this as the field of khipu studies continues to evolve.</p> <p>In the wake of recent allegations of widespread sexual harassment within the field of khipu studies, Andean studies, Anthropology, and academia generally, the OKR board wishes to make it clear that we do not tolerate sexual harassment by members of the board or by those with whom we collaborate. We deplore the role that sexual exploitation and abuse have played in the compilation of this database in the past. We unequivocally condemn all forms of gender-based harassment and abuse. We do not tolerate discrimination based on sexual identity, gender, nationality, or ethnic identity. The OKR recognizes the patriarchal colonialist legacy of Anthropology and related disciplines, and we will actively work against the perpetuation of colonialist norms in Andean Studies.</p> <p>Our goal is to make the field of khipu studies open, inclusive, and safe for all scholars. To achieve that:</p> <ul> <li>We will not collaborate with scholars against whom there are credible allegations of sexual harassment.</li> <li>We will not collaborate with scholars against whom there are credible allegations of bullying or other identity-based discrimination or harassment.</li> <li>We recognize that khipu are not solely Peruvian. We will use language that does not exclude other Andean countries that consider khipu a part of their material heritage.</li> <li>We will include Andean scholars on the board whenever possible.</li> <li>We are in the process of implementing a more neutral khipu identification system that does not privilege the initials of scholars in each khipu name.</li> <li>We will actively work towards making the OKR available to all scholars with interest, recognizing that true accessibility will take time.</li> <li>We will commit to making OKR documentation publicly accessible and available in multiple languages, beginning with English and Spanish.</li> </ul>
Annotation of Metabolites in Stable Isotope Tracing Untargeted Metabolomics via Khipu-web
<p>This is the data and analysis scripts needed to recreate the analyses shown in "Annotation of Metabolites in Stable Isotope Tracing Untargeted Metabolomics via Khipu-web"</p> <p>The abstract of the manuscript summarizes the goal of the paper:</p> <p> </p> <p>Stable isotope tracing is a crucial technique for understanding the metabolic wiring of biological systems, determining metabolic flux through pathways of interest, and detecting novel metabolites and pathways. Despite the potential insights provided by this technique, its application remains limited to a small number of targeted molecules and pathways. Because previous software tools usually require chemical formulas to find relevant features, and the data are highly complex, especially in untargeted metabolomics and when the reactions and metabolites downstream the labeled substrates are poorly characterized. We report here Khipu version 2 and its new user-friendly web application. New functions are added to enhance analyzing stable isotope tracing data including metrics that evaluate peak enrichment in labeled samples, scoring methods to facilitate robust detection of intensity patterns and integrated natural abundance correction. We demonstrate that this approach can be applied to untargeted metabolomics to systematically extract isotope-labeled compounds and annotate the unidentified metabolites.</p> <p> </p> <p>This repository stores the code and data needed to recreate all presented analyses. The code and instructions are in the AnalysisCode.zip. The DDA in the dda_mzML.zip, the MS1 in the dataset_mzml.zip, and the asari results in the AsariResults.zip. The readme is in the AnalysisCode.zip and has more detailed instructions. This directory also has the output data in tabular format for the figures as the figures were mostly made with Excel. </p>
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