So, to emphasize what I mean, consider the following example: You want to enter a chemical sum formula (or an whole equation) into a text, spreadsheet, whatever. Of course, you can abuse some of the already existing tools such as superscript/subscript in a word processor or math mode to get the symbols and format you need.
But, one could think of a more natural way to enter such information and I am sure there are already approaches to do so. Also approaches for data file formats to save this information, ...
Now, are there journals dealing with developing of such methods and approaches?
If you're talking about equation and text formatting, have you considered using LaTeX? It was specifically designed for that. And more and more journals actually have templates for this format (good examples are Bioinformatics and all the IEEE journals and conferences)
If you're talking about equation and text formatting, have you considered using LaTeX? It was specifically designed for that. And more and more journals actually have templates for this format (good examples are Bioinformatics and all the IEEE journals and conferences)
The most usual was is to insert in your text chemical equations as figures imported from a more specific software tool (there are many of those). Regarding a Journal dealing with that... I am not sure. Check Journal of Chemoinformatics, it might be related with your interest.
Thank you for your answers!
The example regarding the entering of chemical information was just an example. I know Latex (and I am using it).
I checked the journals and "Journal of Chemoinformatics" is exactly what I wanted. Thank you, Hegoi!
There are specific drawing programs (for instance, Chewdraw or Conquest) that allow you to draw in 2D, on your terminal, any chemical structure and converts it into a compound formula, a 3D structure, and/or a IUPAC chemical name. It can even be used to search in databases or as input for computational and simulation programs.
Please add our MedChem Designer software to the set of (free) chemical drawing tools.
Concerning chemistry with LaTeX, among all package from the page http://www.ctan.org/topic/chemistry
have a look on this one : http://www.ctan.org/tex-archive/macros/latex/contrib/chemmacros
Please have a look at click2drug.org. You'll find an important list of tools for chemical editing (and many others dedicated to modeling, cheminformatics and bioinfomratics).
syrris.com/batch-products/bioisostere-software
1. Medstere Bioisostere Software Molecule
Medstere Bioisostere Logo
Medstere is innovative bioisostere replacement software designed specifically for medicinal chemists. It shortens lead optimization cycles by suggesting thousands of obvious and non-obvious alternatives to a known lead. By intelligently ranking compounds from the view point of proteins it offers structurally diverse suggestions.
Intelligent: Generates highly innovative ideas for lead molecules in new areas of chemical space, overcoming the 'chemotype trap'.
Extremely accurate: Identifies structurally diverse bioisosteres with or without knowledge of the target protein's structure.
Easy to use: Interface quickly creates a range of potential lead molecules from initial 2D or 3D lead structure and scores them.
Innovative: Medstere ensures that suggested molecules are synthesizable by using fragments from databases of hundreds of thousands of commercially available compounds.
Easy analysis: Visualize results in detail side-by-side, or using powerful new tools to cluster similar chemotypes.
Comprehensive: Medstere comes with a large database of fragments generated from commercially available compounds.
Real time filtering: Invaluable results filtering according to logP, TPSA, Rule of Five, etc. enables rapid selection of new compounds.
Efficient: Helps to ensure that your leads are free from known IP, ADME or toxicity issues.
2. accelrys.com/resource-center/case-studies/archive
Accelrys develops modeling software designed to provide answers to these questions. Accelrys' Cerius2™, a leading simulation and modeling environment, has modules for computing compound properties such as lipophilicity, hydrogen bond donor and acceptor capabilities, and others that are of general interest to pharmaceutical drug development companies (C2.Descriptor+). This program can also compute how well a given set of molecules covers property space (C2.QSAR+). Other modules can be used to enumerate electronic libraries of compounds that provide uniform coverage of property space (C2.AnalogBuilder, C2.LibEngine). These libraries can be controlled so that all members turn out to be chemically synthesizable by practical routes. Cerius2 also has methods for comparing different libraries (C2.LibCompare). In this example, the RSP existing collection against a more ideal hypothetical library. Finally, a subset of compounds can be computed, including examples from both libraries, that provides optimal coverage of property space (C2.Diversity).
Hope this helps.
H Levenson
Hi,
I have always found the Journal of Molecular Biology, Bioinformatics and Journal of Mathematical Biology useful.
Sure. Many. Like Elsevier's Science Journal of Computational Science: http://www.journals.elsevier.com/journal-of-computational-science
Also the J Chem Inf Model (http://pubs.acs.org/journal/jcisd8) publishes a number papers with methodological background
As many people write it before, I agree with this journal : Bioinformatics from Oxford press. http://bioinformatics.oxfordjournals.org/
Of interest may be CML, the chemical markup language.
See http://en.wikipedia.org/wiki/Chemical_Markup_Language , also the list of references and journal cited there.
If I remember correctly, it was also discussed in providing hooks for chemically interesting data, e.g. IR spectra, or results of ab initio calculations, or ...
Several programs provide hooks for CML
Also have a look at Elsvier's Environmental Modelling & Software. Thier scope is rather broad and its a high quality journal.
You should also have a look at the Wiley journal: Wires Computational Molecular Science: http://wires.wiley.com/WileyCDA/WiresJournal/wisId-WCMS.html
1. Computer Physics Communications
2. Journal of Computational Chemistry
I'm not sure how broad of scope you are interested in, but you might also consider these journals for reporting advances in physical modeling and simulation software:
Computational Science & Discovery is an international, multidisciplinary journal focused on scientific advances and discovery through computational science in physics, chemistry, biology and applied science. http://iopscience.iop.org/1749-4699/
and
The ACM Transactions on Modeling and Computer Simulation (TOMACS) provides a single archival source for the publication of high-quality research and developmental results in computer simulation. The subjects of emphasis are discrete event simulation, combined discrete and continuous simulation, as well as Monte Carlo methods. http://tomacs.acm.org/
I guess your question is confusing. What you mean -if i understand well- is designing a "TEXTING" tool..This is not related to natural science or chemistry by any mean..So, you shouldn't look into physics or chemistry Journals..
If you need a way to develop a software to handle chemical or physical problems, don't start with papers, go directly to text books and there are many..Papers usually have a truncated concepts and always written by some one who see them as the "BEST OF THE BEST" otherwise he will not bother himself writing...
If you use LaTeX, include this: \usepackage[version=3]{mhchem} and then you will be able to write reactions nicely. As to publication, look at J Math Chem.
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