Bioinformatics is notoriously complicated, what with its arcane command-line interface, complex workflows, and massive datasets. For the uninitiated, simply installing the software can present a problem. A new paper on the bioRxiv preprint archive describes one possible solution, a bioinformatics-focused package manager called Bioconda. The problem Bioconda attempts to solve is this. Consider the popular package SAMTOOLS, which is used to create and manipulate sequence alignment data files.
Data reproducibility and transparency mean different things to different people, but one aspect involves allowing scientists to view and manipulate the data or code underlying published figures, both to double-check others’ work and to repeat those analyses using custom data. Over the past year, for instance, the open-access journal F1000Research has implemented integrations with Code Ocean and Plotly for viewing and manipulating programming code and figures, respectively.
For this week’s Technology Feature, Michael Eisenstein wrote about the technology, applications, and challenges of nanopore DNA sequencing. In brief, the technology involves threading intact pieces of DNA through a tiny aperture in a membrane or other barrier, through which a current flows. As each base passes, it disrupts that current in a characteristic way, allowing the sequence to be determined.
Muck Rack makes it simple to find people, tweets, or articles that mention any name, keyword, company, hashtag etc. We've compiled this guide to help you make the most of your search.
Selecting a term
Start searching tweets, articles from media outlets, articles mentioned in tweets, journalists'
names, titles and bios with some suggested searches:
Companies or Topics (e.g. iPhone, Microsoft)
Phrases (e.g. "cloud computing") — use quotes to keep the terms together
Twitter handles (e.g. @username) — returns those who have mentioned or replied to
Names (e.g. "David Pogue")
Hashtags (e.g. #sxsw, #london2012)
Bio details (e.g. vegan, Olympics, father)
Muck Rack's Advanced Search allows for many boolean operators.
Find results that mention multiple specified terms, use AND or
+. For example, ensure each result contains both Elon Musk and Mark Zuckerberg by
searching Musk AND Zuckerberg or Musk + Zuckerberg.
Use the operators OR or , to broaden your search when you'd like either of
multiple terms to appear in results. (This is the default behavior of our search when no operators
are used). For example, results will contain either cake or cookie by searching cake OR cookie or cake,cookie
Use NOT or - to subtract results from your search. For
example, searching Disney will yield results about the Walt Disney Company as well as Walt Disney
World Resort. To exclude mentions of Disney World, search for Disney -World or Disney
When using one of these operators with a phrase, enclose it in quotation marks. For example, you can
find results about smartphones excluding Apple's iPhone 4S by searching smartphone -"iPhone
Exact case matching or punctuation
If you're searching for a brand name or keyword that relies on specific punctuation marks or capitalization, you can
find results that match your exact query by adding matchcase: before the keyword you're searching for, like matchcase:E*TRADE .
Use parentheses to separate multiple
boolean phrases. For example, to find journalists talking about having fun in Disney World or
Disneyland, search for ("disney world" OR disneyland) AND fun.
An asterisk can be used to search for any variation of a root word truncated by the asterisk. For example, searching for admin* will return results for administrator, administration, administer, administered, etc.
A near operator is an AND operator where you can control the distance between the words. You can vary the distance the near operation uses by adding a forward slash and number (between 0-99) such as strawberries NEAR/10 "whipped cream", which means the strawberries must exist within 10 words of "whipped cream".