Category: Book Reviews

Reviews of books featuring a summary of the book and links to related material

Feb 09 2015

Book review: Remote Pairing by Joe Kutner

 

jkrp_xlargecoverThis review was first published at ScraperWiki.

Pair programming is an important part of the Agile process but sometimes the programmers are not physically co-located. At ScraperWiki we have staff who do both scheduled and ad hoc remote working therefore methods for working together remotely are important to us. A result of a casual comment on Twitter, I picked up “Remote Pairing” by Joe Kutner which covers just this subject.

Remote Pairing is a short volume, less than 100 pages. It starts for a motivation for pair programming with some presentation of the evidence for its effectiveness. It then goes on to cover some of the more social aspects of pairing – how do you tell your partner you need a “comfort break”? This theme makes a slight reprise in the final chapter with some case studies of remote pairing. And then into technical aspects.

The first systems mentioned are straightforward audio/visual packages including Skype and Google Hangouts. I’d not seen ScreenHero previously but it looks like it wouldn’t be an option for ScraperWiki since our developers work primarily in Ubuntu; ScreenHero only supports Windows and OS X currently. We use Skype regularly for customer calls, and Google Hangouts for our daily standup. For pairing we typically use appear.in which provides audio/visual connections and screensharing without the complexities of wrangling Google’s social ecosystem which come into play when we try to use Google Hangouts.

But these packages are not about shared interaction, for this Kutner starts with the vim/tmux combination. This is venerable technology built into Linux systems, or at least easily installable. Vim is the well-known editor, tmux allows a user to access multiple terminal sessions inside one terminal window. The combination allows programmers to work fully collaboratively on code, both partners can type into the same workspace. You might even want to use vim and tmux when you are standing next to one another. The next chapter covers proxy servers and tmate (a fork of tmux) which make the process of sharing a session easier by providing tunnels through the Cloud.

Remote Pairing then goes on to cover interactive screensharing using vnc and NoMachine, these look like pretty portable systems. Along with the chapter on collaborating using plugins for IDEs this is something we have not used at ScraperWiki. Around the office none of us currently make use of full blown IDEs despite having used them in the past. Several of us use Sublime Text for which there is a commercial sharing product (floobits) but we don’t feel sufficiently motivated to try this out.

The chapter on “building a pairing server” seems a bit out of place to me, the content is quite generic. Perhaps because at ScraperWiki we have always written code in the Cloud we take it for granted. The scheme Kutner follows uses vagrant and Puppet to configure servers in the Cloud. This is a fairly effective scheme. We have been using Docker extensively which is a slightly different thing, since a Docker container is not a virtual machine.

Are we doing anything different in the office as a result of this book? Yes – we’ve got a good quality external microphone (a Blue Snowball), and it’s so good I’ve got one for myself. Managing audio is still something that seems a challenge for modern operating systems. To a human it seems obvious that if we’ve plugged in a headset and opened up Google Hangouts then we might want to talk to someone and that we might want to hear their voice too. To a computer this seems unimaginable. I’m looking to try out NoMachine when a suitable occasion arises.

Remote Pairing is a handy guide for those getting started with remote working, and it’s a useful summary for those wanting to see if they are missing any tricks.

Jan 20 2015

Book review: Sextant by David Barrie

sextantThe longitude and navigation at sea has been a recurring theme over the last year of my reading. Sextant by David Barrie may be the last in the series. It is subtitled “A Voyage Guided by the Stars and the Men Who Mapped the World’s Oceans”.

Barrie’s book is something of a travelogue, each chapter starts with an extract from his diary on crossing the Atlantic in a small yacht as a (late) teenager in the early seventies. Here he learnt something of celestial navigation. The chapters themselves are a mixture of those on navigational techniques and those on significant voyages. Included in the latter are voyages such of those of Cook and Flinders, Bligh, various French explorers including Bougainville and La Pérouse, Fitzroy’s expeditions in the Beagle and Shackleton’s expedition to the Antarctic. These are primarily voyages from the second half of the 18th century exploring the Pacific coasts.

Celestial navigation relies on being able to measure the location of various bodies such as the sun, moon, Pole star and other stars. Here “location” means the angle between the body and some other point such as the horizon. Such measurements can be used to determine latitude, and in rather more complex manner, longitude. Devices such as the back-staff and cross-staff were in use during the 16th century. During the latter half of the 17th century it became obvious that one method to determine the longitude would be to measure the location of the moon relative to the immobile background of stars, the so-called lunar distance method. To determine the longitude to the precision required by the Longitude Act of 1714 would require those measurements to be made to a high degree of accuracy.

Newton invented a quadrant device somewhat similar to the sextant in the late 17th century but the design was not published until his death in 1742, in the meantime Hadley and Thomas Godfrey made independent inventions. A quadrant is an eighth of a circle segment which allows measurements up to 90 degrees. A sextant subtends a sixth of a circle and allows measurements up to 120 degrees.

The sextant of the title was first made by John Bird in 1757, commissioned by a naval officer who had made the first tests on the lunar distance method for determining the longitude at sea using Tobias Meyer’s lunar distance tables.

Both quadrant and sextant are more sophisticated devices than their cross- and back-staff precursors. They comprise a graduated angular scale and optics to bring the target object and reference object together, and to prevent the user gazing at the sun with an unprotected eye. The design of the sextant changed little since its invention. As a scientist who has worked with optics they look like pieces of modern optical equipment in terms of their materials, finish and mechanisms.

Alongside the sextant the chronometer was the second essential piece of navigational equipment, used to provide the time at a reference location (such as Greenwich) to compare to local time to get the longitude. Chronometers took a while to become a reliable piece of equipment, at the end of Beagles 4 year voyage in 1830 only half of the 22 chronometers were still running well. Shackleton’s mission in 1914 suffered even more, with the final stretch of their voyage to South Georgia using the last working of 24 chronometers. Granted his ship, the Endeavour had been broken up by ice and they had escaped to Elephant Island in a small, open boat! Note the large numbers of chronometers taken on these voyages of exploration.

Barrie is of the more subtle persuasion in the interpretation of the history of the chronometer. John Harrison certainly played a huge part in this story but his chronometers were exquisite, expensive, unique devices*. Larcum Kendall’s K1 chronometer was taken by Cook on his 1769 voyage. Kendall was paid a total of £500 for this chronometer, made as a demonstration that Harrison’s work could be repeated. This cost should be compared to a sum of £2800 which the navy paid for the HMS Endeavour in which the voyage was made!

An amusing aside, when the Ordnance Survey located the Scilly Isles by triangulation in 1797 they discovered its location was 20 miles from that which had previously been assumed. Meaning that prior to their measurement the location of Tahiti was better known through the astronomical observations made by Cook’s mission.

The risks the 18th century explorers ran are pretty mind-boggling. Even if the expedition was not lost – such as that of La Pérouse – losing 25% of the crew was not exceptional. Its reminiscent of the Apollo moon missions, thankfully casualties were remarkably low, but the crews of the earlier missions had a pretty pragmatic view of the serious risks they were running.

This book is different from the others I have read on marine navigation, more relaxed and conversational but with more detail on the nitty-gritty of the process of marine navigation. Perhaps my next reading in this area will be the accounts of some of the French explorers of the late 18th century.

*In the parlance of modern server management Harrison’s chronometers were pets not cattle!

Jan 03 2015

Book review: Graph Databases by Ian Robinson, Jim Webber and Emil Eifrem

graphdatabases

This review was first posted at ScraperWiki.

Regular readers will know I am on a bit of a graph binge at the moment. In computer science and mathematics graphs are collections of nodes joined by edges, they have all sorts of applications including the study of social networks and route finding. Having covered graph theory and visualisation, I now move on to graph databases. I started on this path with Seven Databases in Seven Weeks which introduces the Neo4j graph database.

And so to Graph Databases by Ian Robinson, Jim Webber and Emil Eifrem which, despite its general title, is really a book about Neo4j. This is no big deal since Neo4j is the leading open source graph database.

This is not just random reading, we’re working on an EU project, NewsReader, which makes significant use of RDF – a type of graph-shaped data. We’re also working on a project for a customer which involves traversing a hierarchy of several thousand nodes. This leads to some rather convoluted joining operations when done on a SQL database, a graph database might be better suited to the problem.

The book starts with some definitions, identifying the types of graph database (property graph, hypergraph, RDF). Neo4j uses property graphs where nodes and edges are distinct items and each can hold properties. In contrast RDF graphs are expressed as triples which encompass both edges and nodes. In hypergraphs multiple edges can be expressed as a single item. A second set of definitions are regarding the types of graph processing system: graph databases and graph analytical engines. Neo4j is designed to provide good performance for database-like queries, acting as a backing store for a web application rather than an analytical engine to carry out offline calculations. There’s also an Appendix comparing NoSQL databases which feels like it should be part of the introduction.

A key feature of native graph databases, such as Neo4j, is “index-free adjacency”. The authors don’t seem to define this well early in the book but later on whilst discussing the internals of Neo4j it is all made clear: nodes and edges are stored as fixed length records with references to a list of nodes to which they are connected. This means its very fast to visit a node, and then iterate over all of its attached neighbours. The alternative index-based lookups may involve scanning a whole table to find all links to a particular node. It is in the area of traversing networks that Neo4j shines in performance terms compared to SQL.

As Robinson et al emphasise in motivating the use of graph databases: Other types of NoSQL database and SQL databases are not built fundamentally around the idea of relationships between data except in quite a constrained sense. For SQL databases there is an overhead to carrying out join queries which are SQLs way of introducing relationships. As I hinted earlier storing hierarchies in SQL databases leads to some nasty looking, slow queries. In practice SQL databases are denormalised for performance reasons to address these cases. Graph databases, on the other hand, are all about relationships.

Schema are an important concept in SQL databases, they are used to enforce constraints on a database i.e. “this thing must be a string” or “this thing must be in this set”. Neo4j describes itself as “schema optional”, the schema functionality seems relatively recently introduced and is not discussed in this book although it is alluded to. As someone with a small background in SQL the absence of schema in NoSQL databases is always the cause of some anxiety and distress.

A chapter on data modelling and the Cypher query language feels like the heart of the book. People say that Neo4j is “whiteboard friendly” in that if you can draw a relationship structure on a whiteboard then you can implement it in Neo4j without going through the rigmarole of making some normalised schema that doesn’t look like what you’ve drawn. This seems fair up to a point, your whiteboard scribbles do tend to be guided to a degree by what your target system is, and you can go wrong with your data model going from whiteboard to data model, even in Neo4j.

I imagine it is no accident that more recent query languages like Cypher and SPARQL look a bit like SQL. Although that said, Cypher relies on ASCII art to MATCH nodes wrapped in round brackets and edges (relationships) wrapped in square brackets with arrows –>  indicating the direction of relationships:

MATCH (node1)-[rel:TYPE]->(node2)
RETURN rel.property

which is pretty un-SQL-like!

Graph databases goes on to describe implementing an application using Neo4j. The example code in the book is in Java but there appears, in py2neo, to be a relatively mature Python client. The situation here seems to be in flux since searching the web brings up references to an older python-embedded library which is now deprecated. The book pre-dates Neo4j 2.0 which introduced some significant changes.

The book finishes with some examples from the real world and some demonstrations of popular graph theory analysis. I liked the real world examples of a social recommendation system, access control and parcel routing. The coverage of graph theory analysis was rather brief, and didn’t explicit use Cypher which would have made the presentation different from what you find in the usual graph theory textbooks.

Overall I have mixed feelings about this book: the introduction and overview sections are good, as is the part on Neo4j internals. It’s a rather slim volume, feels a bit disjointed and is not up to date with Ne04j 2.0 which has significant new functionality.  Perhaps this is not the arena for a dead-tree publication – the Neo4j website has a comprehensive set of reference and tutorial material, and if you are happy with a purely electronic version than you can get Graph Databases for free (here).

Dec 28 2014

Book review: Maskelyne – Astronomer Royal edited by Rebekah Higgitt

MaskelyneOver the years I’ve read a number of books around the Royal Observatory at Greenwich: books about finding the longitude or about people.

Maskelyne – Astronomer Royal edited by Rebekah Higgitt is unusual for me – it’s an edited volume of articles relating to Nevil Maskelyne by a range of authors rather than a single author work. Linking these articles are “Case Studies” written by Higgitt which provide background and coherence.

The collection includes articles on the evolution of Maskelyne’s reputation, Robert Waddington – who travelled with him on his St Helena trip, his role as a manager, the human computers used to calculate the tables in the Nautical Almanac, his interactions with clockmakers, his relationships with savants across Europe, his relationship with Joseph Banks, and his family life.

The Royal Observatory with its Astronomer Royal was founded by Charles II in 1675 with the goal of making astronomical observations to help with maritime navigation. The role gained importance in 1714 with the passing of the Longitude Act, which offered a prize to anyone who could present a practical method of finding the longitude at sea. The Astronomer Royal was one of the appointees to the Board of Longitude who judged applications. The observations and calculations done, and directed, from the Observatory were to form an important part of successful navigation at sea.

The post of Astronomy Royal was first held by John Flamsteed and then Edmund Halley. A persistent problem to the time of Maskelyne was the publication of the observations of the Astronomers Royal. Flamsteed and Newton notoriously fell out over such measurements. It seems very odd to modern eyes, but the observations the early Astronomers Royal made they essentially saw as their personal property, removed by executors on their death and thus lost to the nation. Furthermore, in the time of Maskelyne the Royal Observatory was not considered the pre-eminent observatory in Britain in terms of the quality of its instruments or observations.

Maskelyne’s appointment was to address these problems. He made the observations of the Observatory available to the Royal Society (the Visitors of the Observatory) on an annual basis and pushed for the publication of earlier observations. He made the making of observations a much more systematic affair, and he had a keen interest in the quality of the instruments used. Furthermore, he started the publication of the Nautical Almanac which provided sailors with a relatively quick method for calculating their longitude using the lunar distance method. He was keenly aware of the importance of providing accurate, reliable observational and calculated results.

He was appointed Astronomer Royal in 1765 not long after a trip to St Helena to make measurements of the first of a pair of Venus transits in 1761, to this he added a range of other activities which including testing the lunar distance method for finding longitude, the the “going” of precision clocks over an extended period and Harrison’s H4 chronometer. In later years he was instrumental in coordinating a number of further scientific expeditions doing things such as ensuring uniform instrumentation, providing detailed instructions for observers and giving voyages multiple scientific targets.

H4 is a primary reason for Maskelyne’s “notoriety”, in large part because of Dava Sobel’s book on finding the longitude where he is portrayed as the villain against the heroic clockmaker, John Harrison. By 1761 John Harrison had been working on the longitude problem by means of clocks for many years. Sobel’s presentation sees Maskelyne as a biased judge, favouring the Lunar distance method for determining longitude acting in his own interests against Harrison.

Professional historians of science have long felt that Maskelyne was hard done by Sobel’s biography. This book is not a rebuttal of Sobel’s but is written with the intention of bringing more information regarding Maskelyne to a general readership. It’s also stimulated by the availability of new material regarding Maskelyne.

Much of the book covers Maskelyne’s personal interactions with a range of people and groups. It details his exchanges with the “computers” who did the lengthy calculations which went into the Nautical Almanac; his interactions with a whole range of clockmakers for whom he often recommended to others looking for precision timepieces for astronomical purposes. It also discusses his relationships with other savants across Europe and the Royal Society. His relationship with Joseph Banks garners a whole chapter. A proposition in one chapter is that such personal, rather than institutional, relationships were key to 18th century science, I can’t help feeling this is still the case.

The theme of these articles is that Maskelyne was a considerate and competent man, going out of his way to help and support those he worked with. To my mind his hallmark is bringing professionalism to the business of astronomy.

In common with Finding Longitude this book is beautifully produced, and despite the multitude of authors it hangs together nicely. It’s not really a biography of Maskelyne but perhaps better for that.

Nov 27 2014

Book review: Linked by Albert-László Barabási

This review was first posted at ScraperWiki.
linkedI am on a bit of a graph theory binge, it started with an attempt to learn about Gephi, the graph visualisation software, which developed into reading a proper grown up book on graph theory. I then learnt a little more about practicalities on reading Seven Databases in Seven Weeks, which included a section on Neo4J – a graph database. Now I move on to Linked by Albert-László Barabási, this is a popular account of the rise of the analysis of complex networks in the late nineties. A short subtitle used on earlier editions was “The New Science of Networks”. The rather lengthy subtitle on this edition is “How Everything Is Connected to Everything Else and What It Means for Business, Science, and Everyday Life”.

In mathematical terms a graph is an abstract collection of nodes linked by edges. My social network is a graph comprised of people, the nodes, and their interactions such as friendships, which are the edges. The internet is a graph, comprising routers at the nodes and the links between them are edges. “Network” is a less formal term often used synonymously with graph, “complex” is more a matter of taste but it implies large and with a structure which cannot be trivially described i.e. each node has four edges is not a complex network.
The models used for the complex networks discussed in this book are the descendants of the random networks first constructed by Erdős and Rényi. They imagined a simple scheme whereby nodes in a network were randomly connected with some fixed probability. This generates a particular type of random network which do not replicate real-world networks such as social networks or the internet. The innovations introduced by Barabási and others are in the measurement of real world networks and new methods of construction which produce small-world and scale-free network models. Small-world networks are characterised by clusters of tightly interconnected nodes with a few links between those clusters, they describe social networks. Scale-free networks contain nodes with any number of connections but where nodes with larger numbers of connections are less common than those with a small number. For example on the web there are many web pages (nodes) with a few links (edges) but there exist some web pages with thousands and thousands of links, and all values in between.
I’ve long been aware of Barabási’s work, dating back to my time as an academic where I worked in the area of soft condensed matter. The study of complex networks was becoming a thing at the time, and of all the areas of physics soft condensed matter was closest to it. Barabási’s work was one of the sparks that set the area going. The connection with physics is around so-called power laws which are found in a wide range of physical systems. The networks that Barabási is so interested in show power law behaviour in the number of connections a node has. This has implications for a wide range of properties of the system such as robustness to the removal of nodes, transport properties and so forth. The book starts with some historical vignettes on the origins of graph theory, with Euler and the bridges of Königsberg problem. It then goes on to discuss various complex networks with some coverage of the origins of their study and the work that Barabási has done in the area. As such it is a pretty personal review. Barabási also recounts some of the history of “six degrees of separation”, the idea that everyone is linked to everyone else by only six links. This idea had its traceable origins back in the early years of the 20th century in Budapest.
Graph theory has been around for a long while, and the study of random networks for 50 years or so. Why the sudden surge in interest? It boils down to a couple of factors, the first is the internet which provides a complex network of physical connections on which a further complex network of connections sit in the form of the web. The graph structure of this infrastructure is relatively easy to explore using automatic tools, you can build a map of millions of nodes with relative ease compared to networks in the “real” world. Furthermore, this complex network infrastructure and the rise of automated experiments has improved our ability to explore and disseminate information on physical networks. For example, the network of chemical interactions in a cell, the network of actors in movies, our social interactions, the spread of disease and so forth. In the past getting such detailed information on large networks was tiresome and the distribution mechanisms for such data slow and inconvenient.
For a book written a few short years ago, Linked can feel strangely dated. It discusses Apple’s failure in the handheld computing market with the Newton palm top device, and the success of Palm with their subsequent range. Names of long forgotten internet companies float by, although even at the time of writing Google was beginning its dominance.
If you are new to graph theory and want an unchallenging introduction then Linked is a good place to start. It’s readable and has a whole load of interesting examples of scale free networks in the wild. Whilst not the whole of graph theory, this is where interesting new things are happening.