[{"id":246,"title":"Bionode - Modular and universal bioinformatics","sha":"8199658b25e657cae1363df4da92f200","user_id":null,"state":"published","body":"\u003e Highly reusable tools and code for bioinformatics, focused on\r\n* [Node.js](http://nodejs.org)/JavaScript to be *\"write once, run anywhere\"*\r\n* Node.js [Streams](https://nodejs.org/api/stream.html) and [Events](https://nodejs.org/api/events.html) for scalable and reactive pipelines\r\n* CLI for easy integration with other tools and languages\r\n\r\nThe [huge decrease in sequencing cost](https://upload.wikimedia.org/wikipedia/commons/b/b7/DNA_Sequencing_Cost_per_Genome_Over_Time.jpg) and consequent [explosion of data](https://www.nlm.nih.gov/about/image/2014CJ_fig_5.png) is reinforcing the need for well tested and scalable tools in biology. It is also causing a [boom in biological web services and databases](https://en.wikipedia.org/wiki/List_of_biological_databases) that often require some data to be processed in the browser. [Bionode](http://bionode.io) provides bioinformatics tools written in Node.js. Bionode is an improvement on other [bio* libraries](http://www.open-bio.org/wiki/Projects#Main_projects) because it can be run anywhere (browsers or servers), it is streamable, and it can be integrated  with other projects and programming languages (each tools is a Node.js module but also comes with a [CLI](https://github.com/bionode/bionode-ncbi#usage)). Bionode tools follow the UNIX philosophy \"do one thing and do it well\". \r\n\r\nAll the development is public and transparent. The code is [MIT](https://opensource.org/licenses/MIT) licensed on [GitHub](http://github.com/bionode), and discussions happen on [Gitter](http://gitter.im/bionode/bionode) and IRC ([freenode #bionode](http://irccloud.com/#!/ircs://irc.freenode.net:6697/%23bionode)). We welcome all kinds of contributions (code, ideas, etc) and we collaborate and integrate with existing projects, such as [Dat](http://dat-data.com) (e.g., [Mozfest 2014 workshop](http://try-dat.com/guide/08-extra-credit.html\r\n)), [BioJS](http://biojs.net) (e.g., [applied together for GSoC 2015](http://biojs.net/gsoc/2015/projects/bionode_biojs.html\r\n)), and [CWL](http://common-workflow-language.github.io\r\n) (e.g., [brainstormed and hacked together at #biohack15 Japan](https://github.com/dbcls/bh15/wiki/Software#reproducible-and-distributable-software-and-data\r\n)). We apply the best practices from web development startups (e.g., [testing, coverage, CI, etc](https://github.com/bionode/bionode-template#principles)) into developing scientific software. Our best practices have [already inspired other projects](https://github.com/hydronode). We have a [small community](https://www.dropbox.com/s/njgeis4e1urolud/Screenshot%202015-09-30%2015.06.19.png?dl=0) but need more contributors.\r\n\r\n* [Bionode website](http://bionode.io)\r\n* [Wurmlab website](http://wurmlab.github.io)\r\n* [Bionode GitHub repository](http://github.com/bionode)\r\n* [Bionode Gitter chat room](http://gitter.im/bionode/bionode)\r\n* [Online shell to try Bionode](http://try.bionode.io)\r\n* [Dat Mozfest14 workshop with Bionode chapter (8)](http://try-dat.com)\r\n* [BioJS GSoC15 page with Bionode project ideas](http://biojs.net/gsoc/2015/)\r\n* [Recent talk at biocoders meetup in Cambridge](http://bmpvieira.com/biocoders15a)\r\n","created_at":"2015-09-30T21:04:51.709Z","updated_at":"2015-10-01T06:00:27.295Z","zenodo_id":63050,"doi":"http://dx.doi.org/10.5281/zenodo.31637","subject":null,"tags":["open research accelerator","bionode","bioinformatics","biology","node.js","javascript"],"vote_count":0,"view_count":1,"score":0.1,"deleted":false,"muted":false,"tweeted":true,"attachment_file_name":"bionode-logo.min.png","attachment_content_type":"image/png","attachment_file_size":18044,"attachment_updated_at":"2015-09-30T21:04:51.382Z"},{"id":448,"title":"Effects of temperature on alcohol tolerance of microbes","sha":"aa69dd7fcd1632e75f773f87ae384ca5","user_id":null,"state":"published","body":"It has been established that dissolution of membrane lipids plays a role in the toxicity of ethanol and butanol to micro-organisms; a matter of particular importance for the production of bio-alcohol fuels using fermentation by microbial activity. However, solubility is a phenomenon heavily governed by temperature.\r\nIt follows that microbial tolerance of these substances will tend to vary with temperature, a phenomenon that has not been studied outside of a narrow range of temperatures in which fermentation is typically conducted, largely because fermentation rate is optimized within that range. However, the main costs involved in bio-alcohol production are feedstock material followed by separation costs. The former of these cost factors is determined by fermentation yield relative to mass and the latter is determined by alcohol product purity which is in turn governed by alcohol tolerance. Fermentation rate only affects reactor sizing, a moderate factor in capital cost with little bearing on operating cost. Hence, compromising fermentation rate in pursuit of alcohol tolerance by exploring unconventional temperature ranges could potentially offer improvements in overall economic performance of bio-alcohol production. ","created_at":"2018-03-22T12:09:37.645Z","updated_at":"2018-05-09T07:40:31.832Z","zenodo_id":1208713,"doi":"https://doi.org/10.5281/zenodo.1208713","subject":null,"tags":["biology","biofuels","fuel"],"vote_count":1,"view_count":1,"score":1.1,"deleted":false,"muted":false,"tweeted":true,"attachment_file_name":null,"attachment_content_type":null,"attachment_file_size":null,"attachment_updated_at":null},{"id":140,"title":"Naturalness of Atheism and Unnaturalnes of Religion","sha":"4ed82f88af3d32867a5489847a4fb334","user_id":257,"state":"published","body":"The standard model of Cognitive Science of Religion (CSR) explains religion as some kind of natural phenomenon. Religious ideas and beliefs are considered as natural not only in the sense of their foundation on cognitive processes and mechanisms, but also as obvious, intuitive, and in some sense inevitable. What is more CSR suggests that religious ideas and beliefs are more natural and evident than atheism. In consequence atheism is considered as unnatural cultural phenomenon which requires special conditions, first of all high development of education and science, in the modern times associated with the Enlightenment. However, biological and evolutionary approaches show that the human being is a species which focuses on natural, sensual information and behaviors which are strategic for survival. Therefore, how can we connect natural selection with religious beliefs which are counter-intuitive and unnatural? Here I would like to show that naturalness of religion hypothesis is not compatible with biological long-orientation perspective. Religion was useful tool after agricultural revolution – however, not for transmission of good moral behavioral patterns. Its main aim was consolidation and strengthening in-group trust and internal network for the purpose of inter-group conflicts and aggression at the level of large groups.   ","created_at":"2015-04-05T16:35:41.347Z","updated_at":"2015-04-10T19:22:24.186Z","zenodo_id":26413,"doi":"http://dx.doi.org/10.5281/zenodo.16628","subject":null,"tags":["atheism","religion","evolution","biology","morality"],"vote_count":2,"view_count":1,"score":2.1,"deleted":false,"muted":false,"tweeted":false,"attachment_file_name":null,"attachment_content_type":null,"attachment_file_size":null,"attachment_updated_at":null},{"id":451,"title":"Microbial butanol tolerance: mediated by toxicity or by phase equilibrium?","sha":"ea407c9f242be9b2102d68134bc245bb","user_id":null,"state":"published","body":"It is conventionally assumed that the achievable concentration of a bio-alcohol molecule by fermentation is limited by the toxicity of that molecule to the micro-organisms producing it. In the case of ethanol, for example, extremely high titers have been achieved by developing resistant strains of micro-organism. Butanol, conversely, has proven remarkably stubborn to this same sort of progression. Despite widespread efforts, concentration above 2% have not been achieved. \r\n2% also happens to be the limit of solubility of butanol in water. It seems intuitive that intra-cellular phase separation would result in highly toxic localized concentrations of butanol, and generally disrupt material transport through cell membranes. This would suggest that butanol titers are fundamentally limited by phase equilibrium and that conventional research to improve butanol tolerance will prove fruitless. \r\nThis hypothesis could be tested experimentally in one of two ways. Firstly, ethanol-producing organisms could be cultivated in a 2% butanol solution. If toxicity is severe then they would be highly inhibited in this environment but if phase equilibrium is the limit then they will cope well. Alternatively, higher temperatures improve solubility. Hence, if butanol tolerance increases with temperature it can be inferred that solubility is limiting.","created_at":"2018-04-05T11:33:47.204Z","updated_at":"2020-07-17T13:07:43.841Z","zenodo_id":1219005,"doi":"https://doi.org/10.5281/zenodo.1219005","subject":null,"tags":["butanol","bio-fuels","biology"],"vote_count":1,"view_count":1,"score":1.1,"deleted":false,"muted":false,"tweeted":true,"attachment_file_name":null,"attachment_content_type":null,"attachment_file_size":null,"attachment_updated_at":null},{"id":1861,"title":"The Biological Rationality of Racial Fetishes","sha":"86c69daa76f4467c19ec017327e411e4","user_id":null,"state":"published","body":"Sexual racism is a problematic feature of dating and pair-bounding preferences. It is seen as reinforcing racial stereotypes and dating hierarchies (Bedi, 2015) among majority ethnicities. Racial fetishization has subjected minority women to harassment (Buchanan et al. 2018), violence (Olive, 2012), and sexual objectification (Zhang et al. 2024).\r\n\r\nMany researchers have written about the ethical issues of racial fetishes, but few have attempted to explain the cause within the context of biology. The Biological Rationality of Racial Fetishes seeks to expound a biological explanation for this phenomenon.  Racial fetishes could be viewed as an adaptive heuristic to avoid inbreeding. Inbreeding is associated with an increased incidence of genetic disorders (Alvarez et al. 2011).\r\n\r\nThis concept is a two-tiered sorting mechanism that relies on phenotypical differences and cultural stereotypes, the assumption being that if a potential mate has a different skin color, accent, bone structure, and or cultural background, there are no familial ties. These differences signal to the potential suitor that they will avoid the risk of inbreeding.\r\n\r\nThere is no excuse for the suboptimal societal outcomes of race-based sexual objectification, but this is merely an attempt to find a biologically rational explanation.","created_at":"2024-10-13T23:47:36.379Z","updated_at":"2024-10-17T06:00:22.216Z","zenodo_id":13942990,"doi":"https://doi.org/10.5281/zenodo.13942990","subject":null,"tags":["mating","dating","sexual racism","biology","genetic diversity","inbreeding","fetishes","heuristic"],"vote_count":0,"view_count":1,"score":0.1,"deleted":false,"muted":false,"tweeted":false,"attachment_file_name":null,"attachment_content_type":null,"attachment_file_size":null,"attachment_updated_at":null},{"id":31,"title":"Does transpiration in hyperaccumulator Pteris vittata mediate asenic translocation from the roots to fronds via xylem?","sha":"3089ef1924d56ecfe40c378469d70bf4","user_id":79,"state":"published","body":"Since the first arsenic (As) hyperaccumulator _Pteris vittata_ was discovered by Ma et al.(2001), we have clarified somewhat in As detoxification in this fern. It is believed that _P. vittata_, as a “model fern” for As study, may take up arsenate (AsV) and arsenite (AsIII) via phosphate transporters (PHTs) and aquaglyceroporins (AQGPs) respectively similar to _Oryza sativa_ and _Arabidopsis thaliana_. Although Indriolo et al.(2010) reported that AsIII transporter PVACR3 mediates AsIII sequestration in the vacuoles of _P. vittata_ fronds, result from Chen et al.(2013) showed different alternative that AsIII is likely to be pumped into apoplasts. One interesting question is that how _P. vittata_ translocates AsIII from the roots to fronds, resulting in up to 2.3% As in _P. vittata_ fronds.\r\nBased on the fact that As promotes _P. vittata_ growth even though hundreds of ppm As is amended, without adverse effects, and pinnae accumulates a high content of As, I think whether As translocation in _P. vittata_ is mediated by transpiration via xylem. When _P. vittata_ was exposed to As, it grew better than that of the condition without As amendation, and it tolerated to drought condition. We thus should answer the potential roles of transpiration in arsenic translocation in _P. vittata_.","created_at":"2015-02-13T10:03:06.901Z","updated_at":"2015-02-20T04:34:56.778Z","zenodo_id":22160,"doi":"http://dx.doi.org/10.5281/zenodo.15095","subject":null,"tags":["biology","arsenic","hyperaccumulator","pteris","vittata"],"vote_count":1,"view_count":1,"score":1.1,"deleted":false,"muted":false,"tweeted":false,"attachment_file_name":null,"attachment_content_type":null,"attachment_file_size":null,"attachment_updated_at":null},{"id":23,"title":"Reanimation of Australian Megafauna, Extinct Species and New Zealand Moas","sha":"5d87b73cfbbd112200914f3638f5f3af","user_id":45,"state":"published","body":"After the arrival of the first humans, Indigenous Australians, to the island continent, the previous megafauna became extinct.  As many samples are still extant, deriving DNA samples or fragments and reverse engineering, through multiple generations could allow us to recreate these fauna, or at the very least, increase our understanding of development, evolution and reproductive technology. It will also increase our technical know how for the development of useful synthetic organisms","created_at":"2015-02-11T01:57:22.473Z","updated_at":"2015-05-27T20:43:01.766Z","zenodo_id":21947,"doi":"http://dx.doi.org/10.5281/zenodo.15013","subject":null,"tags":["synthetic","biology","genetics","reanimation","molecularbiology","extinction"],"vote_count":2,"view_count":1,"score":2.1,"deleted":false,"muted":false,"tweeted":false,"attachment_file_name":null,"attachment_content_type":null,"attachment_file_size":null,"attachment_updated_at":null},{"id":143,"title":"Naturalness of Atheism and Supernaturalness of Religion - A Role for Theological Science","sha":"c4fcf79b9c0be4b2b24ee2baa941a221","user_id":540,"state":"published","body":"Scientific approaches (\"science\" narrowly defined as the \"sciences of nature\") metaphysically exclude divine effects as appropriate--in other words, science itself is structured to exclude divine action (pragmatically). The problem with the \"natural\" study of religion is that religion cannot be reduced to its natural causes and effects. This is precisely because divine causes and effects are the source and telos of religious life, with natural causes being more appropriately \"effects which follow from divine causes\". Science can contribute, because of its structure, studying natural phenomena associated with religion understood as natural phenomena and not as divine phenomena. Therefore, the word \"natural\" must be defined here as \"strictly scientifically natural\", suggesting that atheism is a strictly scientifically natural belief (excluding divinity not only pragmatically but substantially), whereas religion, limited to strictly scientific investigation, is \"natural\" because of its natural effects, but points to something outside of strictly natural explanations. The word \"unnaturalness\" applied to religion by [konrad szocik](/users/76d3c51025e2ea94f969165c2ad98be7) signified the opposite of only a strictly scientific \"naturalness\". A more appropriate word than \"unnaturalness\" would be \"supernaturalness\". This word is more proper to the object of study (religion) and is not contradictory to \"natural\" but suggests explanatory plausibility \"outside\" or beyond the structure of nature, suggesting reality beyond nature. Here is where theology might begin to have significant input.","created_at":"2015-04-10T18:35:46.345Z","updated_at":"2015-04-12T06:01:06.958Z","zenodo_id":26806,"doi":"http://dx.doi.org/10.5281/zenodo.16762","subject":null,"tags":["religion","atheism","science","philosophy","evolution","biology","morality"],"vote_count":0,"view_count":1,"score":0.1,"deleted":false,"muted":false,"tweeted":false,"attachment_file_name":null,"attachment_content_type":null,"attachment_file_size":null,"attachment_updated_at":null}]