Planes, Trains, and Organic Syntheses
Riders of commuter trains are accustomed to using maps like those produced by the London Underground:
These maps are capable of condensing large amounts of information into a useful package. Transit map representations, known more generally as graph or network representations, are especially good at revealing the big picture, although their applications are numerous and can be found these days just about anywhere you find large datasets.
All Aboard
Organic synthesis has proven itself an excellent fit for graph modeling, depiction, and analysis approaches. For example, in 2012 a team led by Bartosz Grzybowski showed ho...
Source: Depth-First - April 25, 2013 Category: Chemists Authors: Richard Apodaca Source Type: blogs
Free Access to ACS Publications and Why You Can't Have It (Yet)
Although not widely-known, the American Chemical Society permits unlimited, free article downloads across its vast journal lineup without a subscription thanks to the Articles on Request program (AoR). Of course there is a catch, explained below, but the official ACS Publications policy is that a significant portion of its collection can in principle be downloaded by anyone for free.
The only problem is that despite the longstanding official position of ACS Publications, its network hasn't been granting access to content eligible for free download under the AoR program. Read on for more about my ongoing efforts to get to ...
Source: Depth-First - April 18, 2013 Category: Chemists Authors: Richard Apodaca Source Type: blogs
Copyright for Chemists: A Failed Test of ACS Articles on Request
The recent article Copyright for Chemists led to this comment from dzrlib:
Are you aware that the ACS provides the corresponding
author with a special URL that can be posted on an institutional website which allows 50 downloads during the first year after it first appears and unlimited downloads after the first year?
The ACS Publications Articles on Request program entitles corresponding authors some possibly useful options for distributing their papers post-publication:
"... a link that provides for up to 50 free e-prints of the final published article during the first 12 months following online publication."
Unlimite...
Source: Depth-First - April 11, 2013 Category: Chemists Authors: Richard Apodaca Source Type: blogs
Copyright for Chemists: Promoting Reuse through Open Licensing
This article explains why you might want to be concerned about reuse of your scientific work and ways you can help ensure that it takes place.
Licenses: Selectively Transfer Some of Your Rights
Governments grant citizens the right to control how their works are reused through copyright. As scientists, these rights are extended to you every time you publish a paper.
Although many organizations such as ACS Publications insist on extracting exclusive copyright from authors as a condition for publication, there is a better way.
As a copyright holder, you can license your work. In doing so, you retain all ownership rights b...
Source: Depth-First - April 11, 2013 Category: Chemists Authors: Richard Apodaca Source Type: blogs
Evernote as an Electronic Lab Notebook (ELN)
Conclusions
For labs with minimal requirements around special data types and electronic signatures, Evernote offers much to like as a replacement for a paper notebook or expensive ELN system. For others with more specific needs, paper or a dedicated ELN system will be the only options. (Source: Depth-First)
Source: Depth-First - April 11, 2013 Category: Chemists Authors: Richard Apodaca Source Type: blogs
Solving Organic Chemistry's Oldest Problem
According to a recent editorial by Rick Danheiser, 3-5% of the procedures submitted for review by Organic Syntheses are rejected "due to the inability of the checkers to satisfactorily reproduce the results of their submitters." During the period 1982-2005 the rejection rate was about 12%.
Organic Syntheses was founded to address organic chemistry's oldest and most persistent problem - documenting and reproducing synthetic procedures. From Danheiser's editorial, it's clear that more work, and possibly a better approach, is needed.
Worse Than It Looks
A failure rate of 3-12% may sound small, but consider the pool from wh...
Source: Depth-First - April 11, 2013 Category: Chemists Authors: Richard Apodaca Source Type: blogs
Chemists: How Do You Keep Current with the Literature?
Whether you know it or not, one of your biggest problems as a chemist is keeping current with the chemical literature. Missing one key paper can make the difference between breakthrough and heartbreak.
The explosive growth rate of the chemical literature makes it increasingly difficult to keep up. From 1997 to 2007, the number of new documents indexed by Chemical Abstracts Service every year doubled to 1.72 million. That's nearly 5,000 documents every day, a rate that in turn doubles every ten years or so. Of course, all of this new content sits on top of the tens of millions of documents already published over the last c...
Source: Depth-First - April 11, 2013 Category: Chemists Authors: Richard Apodaca Source Type: blogs
Chemical Structure Copy and Paste Problems
Conclusions
Round trip editing remains an essential capability for many chemists today. Although sticking within a narrow band of software components generally gives good results, straying outside this configuration can lead to problems quickly.
My current work with ChemWriter has led me to ask to what extent round-trip editing of chemical content is a problem that still needs fixing. If you'd be interested in sharing your experiences either in the comments section or via email, I'd be very interested in hearing from you. (Source: Depth-First)
Source: Depth-First - April 11, 2013 Category: Chemists Authors: Richard Apodaca Source Type: blogs
A Second Failed Test of ACS Articles on Request
Please see the revised post, A Third Failed Test of ACS Articles on Request and How to Help. Although the introduction, conclusions and comments section of the post below may be useful, the links and discussion around them should be disregarded.
A recent post described the lack of public author-oriented documentation for the ACS Articles on Request (AoR) program. For the unfamiliar, AoR is supposed to provide free access to any article published in an ACS Publication:
... the ACS Articles on Request service allows an author's article to be accessed without restriction 12 months after web publication. ACS authors may e-ma...
Source: Depth-First - April 11, 2013 Category: Chemists Authors: Richard Apodaca Source Type: blogs
A Third Failed Test of ACS Articles on Request and How to Help
A previous post detailed my failed attempt to test a rather interesting if not well-known program offered by ACS to corresponding publication authors: "free access" to final published articles after 12 months under the Articles on Request (AoR) program.
In that post I made a mistake that I'll attempt to correct here. Although it doesn't affect my conclusion - that the AoR unlimited "free access" provision doesn't seem to work after 12 months - my mistake does affect those who are trying to repeat my observations.
My mistake was not checking the publication date for the AoR article links I tested. The articles were less t...
Source: Depth-First - April 11, 2013 Category: Chemists Authors: Richard Apodaca Source Type: blogs
Chemists: What Has LinkedIn Done For You Lately?
Developing a network of contacts is often cited as career advice to chemists. Sometimes, LinkedIn is suggested as a good service for doing so.
A recent post describing why one user quit LinkedIn altogether got me thinking about how useful this service is in practice. An older D-F post talked about some problems with LinkedIn forums - specifically, the limitations of investing time and effort on closed discussion forums with a limited audience.
Given the currently underperforming chemistry job market, and the often-cited connection between LinkedIn and finding a job, it seems reasonable to ask chemists - what has LinkedIn...
Source: Depth-First - March 2, 2013 Category: Chemists Authors: Richard Apodaca Source Type: blogs
Copyright for Chemists
Here's a simple question: who "owns" your papers after they're published in a journal? The answer depends on the journal. But if you're like most chemists, the publisher owns your article. Period. You are legally allowed to redistribute your article only under terms given by the publisher. Any other use is punishable by law.
Why should this matter? After all, as long as colleagues and hiring/promotion committees can access your articles, that's all that really matters - right?
Re-Thinking the Permanence of Journals
Although it may seem impossible, your favorite journal's days may be numbered. Over the last several years...
Source: Depth-First - March 2, 2013 Category: Chemists Authors: Richard Apodaca Source Type: blogs
Copyright for Chemists: How to Free Your Supporting Information
This article explains how to make the most of those rights.
Why Supporting Information Matters
Supporting information is a strange, magical beast in chemistry. During manuscript preparation, the compilation of supporting information is often regarded as a necessary, unpleasant chore. Yet after publication, the content of a well-written supporting information package can become far more valuable than the published paper itself.
Chemists value the ability to repeat, modify, and adapt an experimental protocol almost as highly - if not more so - than the ability to read the author's summary and interpretation on the subject...
Source: Depth-First - March 2, 2013 Category: Chemists Authors: Richard Apodaca Source Type: blogs
Anonymous Science and the Survival of BlogSyn
BlogSyn is a recently-launched post-publication review site for synthetic organic procedures. It has been discussed widely on blogs and Twitter, and was recently featured on Nature News.
From the moment the homepage loads, you’ll realize this is no Organic Syntheses. However, the most significant difference lies not in what’s being revealed, but what remains hidden.
Blogging Experimental Chemistry is so 2005
If BlogSyn merely contained experimental chemistry writeups published directly to the Web, it would be interesting, but hardly unique. Useful Chemistry and the UsefulChem Wiki...
Source: Depth-First - February 23, 2013 Category: Chemists Authors: Richard Apodaca Source Type: blogs
