Re: [BlueObelisk-discuss] SciPost-Chemistry (Diamond Access journals in chemistry)
The journal Quantum (https://quantum-journal.org) is taking a somewhat similar approach, though they have not been able to get the cost to zero...though you can pay nothing (more of an honor system). See https://quantum-journal.org/update-on-quantums-publication-fees/ for details. It is an interesting approach, journals for researchers run by researchers. The hard part is to get enough "rich" researchers to not pay for open- or closed access (library pays). A lot of journals are driven by professional societies. To get around those, it would mean increasing memberships to the professional societies, i.e. a bit more socialist approach. So, changing business models is not just a publisher issue I think. If we could convince one society to go free open-access, it might help get the transformation started. Bert On Mon, May 10, 2021 at 12:14 PM Peter Murray-Rust wrote: > Introducing Jean-Sebastian Caux, > > J-S is a theoretical condensed matter physicist developing the strategy > and practice of Diamond Access (no-fee publication/reading) in science. > This started with physics and he is now adding chemistry. I think BO will > be a great place to find volunteers and information. > > He writes: > > > > Separately, on the SciPost side, here follow a couple of points worth > sharing. > > After establishing our activities in Physics, we'd really like to extend > our services to the community in Chemistry. > > The idea is to apply precisely the same guiding principles > (not-for-profit; academics-led; open refereeing etc, see > https://scipost.org/about) while developing the Chemistry branch. As a > kind of separate note, it's important to understand that SciPost is > proposing a very different business model than those currently discussed > (APCs, etc). The details of this are explained at > https://scipost.org/finances/business_model/ . > > We have already defined a couple of journals, most importantly SciPost > Chemistry (see https://scipost.org/SciPostChem/about) which we would like > to breathe life into. > > The most important foundation stone for this is to build an Editorial > College in Chemistry. We already have a handful of people (see > https://scipost.org/colleges/chemistry) but we're looking for 30 - 50 > more to give proper momentum. Fellows should be academics with very high > reputation and with their heart in the right place as far as reforming > academic publishing is concerned. The workflow for Fellows is summarized at > https://scipost.org/submissions/editorial_workflow (the official by-laws > are at https://scipost.org/EdCol_by-laws). > > > > It is clear that "transformational agreements" , where funders pay the OA > costs (APCs) create more problems than they solve. If you are not employed > by a rich, Northern, university then you can't publish. I'm working with > groups in India and Latin America and it's clear we shall only be able to > publish in a Diamond Access journal. APCs of 2000 - 5000 USD are completely > beyond academics in the Global South or scientists not employed in rich > institutions (I am retired). I think the TAs allow publishers to increase > charges enormously and are globally and socially divisive. > > The answer is Diamond journals and preprints. > > I am working with J-S to search and index equations in physics journals > (it could also apply to chemical physics and physical chemistry). The > goals include: > * ontological help for authors > * novel search tools for readers > > If you believe that Diamond journals are the way forward or feel that the > Global South and non-academics get a bad deal from current publishing then > please join us. > > P > > -- > "I always retain copyright in my papers, and nothing in any contract I > sign with any publisher will override that fact. You should do the same". > > Peter Murray-Rust > Reader Emeritus in Molecular Informatics > Yusuf Hamied Department of Chemistry > University of Cambridge > CB2 1EW, UK > +44-1223-336432 > ___ > Blueobelisk-discuss mailing list > Blueobelisk-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss > ___ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
Re: [BlueObelisk-discuss] Software for ligands
That's a nice overview paper. Started to look more into descriptors, so happy to see the listing of tools one can start from. Some of the web components have been integrated into MongoChem ( https://openchemistry.kitware.com/). Here we use a greatly extended version of Marcus' Chemical Json (reusing some of the CML naming conventions) to generate data and populate a MongoDB. The computational chemistry app used here is NWChem, for which we now have a CJson writer directly in the code (using an open source son fortran writer) and an extensive Python script (which I need to integrate into cclib at some point in the near future). Bert On Thu, Aug 18, 2016 at 5:06 AM, Rajarshi Guha wrote: > There is a nice listing of open tools by Pirhadi et al and covers the > spectrum from cheminformatics to computational chemistry > > http://www.sciencedirect.com/science/article/pii/S1093326316301188 > > On Thu, Aug 18, 2016 at 5:13 AM, Peter Murray-Rust > wrote: > >> I have been talking with the Computational Crystallography group in >> Cambridge/LMB who develop ligand dictionaries for protein crystallography >> and are building their system with Open software (and Open data from >> Crystallography Open Database). >> >> I have suggested that there are Open tools that they may not yet have >> discovered. They have needs for (at least): >> * 2-D chemical editor and display >> * 3-D editor >> * atom typing >> * computational chemistry (e.g. DFT) >> * chemical database software >> >> They have filled some of this themselves, and use RDKIT, but would >> benefit from other components. I pointed them at JChempaint - which has >> matured a lot since I last used it. I have also suggested NWChem. >> >> I am not up-to-date with all the Open software. Do we have a list of >> tools in this area? If not, perhaps people can respond to the list? It >> would be a useful update. >> >> >> -- >> Peter Murray-Rust >> Reader in Molecular Informatics >> Unilever Centre, Dep. Of Chemistry >> University of Cambridge >> CB2 1EW, UK >> +44-1223-763069 >> >> >> -- >> >> ___ >> Blueobelisk-discuss mailing list >> Blueobelisk-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss >> >> > > > -- > Rajarshi Guha | http://blog.rguha.net > NIH Center for Advancing Translational Science > > > -- > > ___ > Blueobelisk-discuss mailing list > Blueobelisk-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss > > -- ___ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
Re: [BlueObelisk-discuss] Google Summer of Code
Just look dat cclib. Marcus and I worked on parsing everything in an NWChem output via a Python script, and putting the data in a Chemical JSON format for NWChem. I probably should contribute some of this here. Also have a Fortran90 Chemical JSON writer that allows QC codes to write out directly to Chemical JSON. Looking to build a C++ analogue as both will cover most codes. Bert On Tue, Mar 1, 2016 at 7:56 AM, Geoffrey Hutchison wrote: > > OpenChemistry has been accepted into the Google Summer of Code for 2016 - > including Open Babel, Avogadro, cclib and 3DMol.js > https://summerofcode.withgoogle.com/organizations/6290185763422208/ > http://wiki.openchemistry.org/GSoC_Ideas_2016 > > If you are a student and interested in doing open chemistry software > development this summer (or know of someone who is), we're definitely > interested in good proposal ideas. > > Looking forward to a summer of great science! > > Cheers, > -Geoff > > -- > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 > ___ > Blueobelisk-discuss mailing list > Blueobelisk-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss > -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140___ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
[BlueObelisk-discuss] BODR covalent radii patch (all elements)
Hi, I have updated the covalent radii for all 118 elements following the definition of one consistent set of radii published Pyykko and Atsumi in Chem. Eur. J. published in 2009. This addresses all elements for which the radii were not given (mainly heavy elements), and updates others. The git pull request can be found at https://github.com/egonw/bodr Please peer review, comment, and apply. Thanks, Bert -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121054471&iu=/4140/ostg.clktrk___ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
